http://publicationslist.org/data/r.siezen/atom.xml Roland Siezenhttp://publicationslist.org/r.siezen$basepathfavicon.icoRecent additions to Roland Siezen's PublicationsList.org pagehttp://publicationslist.org/publications.png2011-03-18T14:50:43Z http://publicationslist.org/r.siezen/refid161 2011-03-18T14:45:16Z

A common bacterial strategy to cope with stressful conditions is the activation of alternative sigma factors that control specific regulons enabling targeted responses. In the human pathogen Bacillus cereus, activation of the major stress-responsive sigma factor σ(B) is controlled by a signalling route that involves the multi-sensor hybrid histidine kinase RsbK. RsbK-type kinases are not restrict...<br/><br/>Mark de Been, Christof Francke, Roland J Siezen, Tjakko Abee (2011) <i>Microbiology</i> <i></i> <i></i> 157: Pt 1 3-12<br/>

http://publicationslist.org/r.siezen/refid151 2011-03-18T14:43:30Z

The "Harlingen" IS6110 restriction fragment length polymorphism (RFLP) cluster has linked over hundred tuberculosis cases in The Netherlands since 1993. Four Mycobacterium tuberculosis isolates that were epidemiologically linked to this cluster had different spoligotype patterns as well as slightly divergent IS6110 profiles, compared to the majority of the isolates. Sequencing of the direct repeat...<br/><br/>Anita C Schürch, Kristin Kremer, Albert Kiers, Martin J Boeree, Roland J Siezen, Dick van Soolingen (2011) <i>J Clin Microbiol</i> <i></i> <i></i> : <br/>

http://publicationslist.org/r.siezen/refid150 2011-03-18T14:43:30Z

Lactococcus lactis produces lactic acid and is widely used in the manufacturing of various fermented dairy products. However, the species is also frequently isolated from non-dairy niches, such as fermented plant material. Recently, these non-dairy strains have gained increasing interest, as they have been described to possess flavour-forming activities that are rarely found in dairy isolates and ...<br/><br/>Roland J Siezen, Jumamurat R Bayjanov, Giovanna E Felis, Marijke R van der Sijde, Marjo Starrenburg, Douwe Molenaar, Michiel Wels, Sacha A F T van Hijum, Johan E T van Hylckama Vlieg (2011) <i>Microb Biotechnol</i> <i></i> <i></i> : <br/>

http://publicationslist.org/r.siezen/refid152 2011-03-18T14:43:30Z

The Beijing genotype family is an epidemiologically important sub-group of Mycobacterium tuberculosis. It has been suggested that the high frequency of the Beijing isolates in some areas could be explained by selective advantages. Some evidence suggests that the emerging and most frequently isolated "Typical Beijing" lineage has the ability to circumvent BCG-induced immunity. To investigate the ph...<br/><br/>Anita C Schürch, Kristin Kremer, Robin M Warren, Nguyen V Hung, Yanlin Zhao, Kanglin Wan, Martin J Boeree, Roland J Siezen, Noel H Smith, Dick van Soolingen (2011) <i>Infect Genet Evol</i> <i></i> <i></i> : <br/>

http://publicationslist.org/r.siezen/refid159 2011-03-18T14:45:16Z

A novel 51-kb conjugative transposon of Lactococcus lactis, designated Tn6098, encoding the capacity to utilize α-galactosides such as raffinose and stachyose, was identified and characterized. Alpha-galactosides are a dominant carbon source in many plant-derived foods. Most dairy lactococcus strains are unable to use α-galactosides as a growth substrate, yet many of these strains are known to h...<br/><br/>Ronnie Machielsen, Roland J Siezen, Sacha A F T van Hijum, Johan E T van Hylckama Vlieg (2011) <i>Appl Environ Microbiol</i> <i></i> <i></i> 77: 2 555-563<br/>

http://publicationslist.org/r.siezen/refid153 2011-03-18T14:43:30Z

Roland J Siezen (2011) <i>Microb Biotechnol</i> <i></i> <i></i> 4: 1 1-7<br/>

http://publicationslist.org/r.siezen/refid154 2011-03-18T14:43:30Z

Anita C Schürch, Roland J Siezen (2010) <i>Microb Biotechnol</i> <i></i> <i></i> 3: 6 628-633<br/>

http://publicationslist.org/r.siezen/refid149 2011-03-18T14:43:30Z

The genus Lactobacillus includes a diverse group of bacteria consisting of many species that are associated with fermentations of plants, meat or milk. In addition, various lactobacilli are natural inhabitants of the intestinal tract of humans and other animals. Finally, several Lactobacillus strains are marketed as probiotics as their consumption can confer a health benefit to host. Presently, 15...<br/><br/>Ravi Kant, Jochen Blom, Airi Palva, Roland J Siezen, Willem M De Vos (2010) <i>Microb Biotechnol</i> <i></i> <i></i> : <br/>

http://publicationslist.org/r.siezen/refid148 2011-03-18T14:43:30Z

Gene regulatory networks can be reconstructed by combining transcriptome data from many different experiments to elucidate relations between the activity of certain transcription factors and the genes they control. To obtain insight in the regulatory network of Lactobacillus plantarum, microarray transcriptome data from more than 70 different experimental conditions were combined and the expressio...<br/><br/>Michiel Wels, Lex Overmars, Christof Francke, Michiel Kleerebezem, Roland J Siezen (2010) <i>Microb Biotechnol</i> <i></i> <i></i> : <br/>

http://publicationslist.org/r.siezen/refid6 2011-03-18T14:46:04Z

A common bacterial strategy for monitoring environmental challenges is to use two-component systems, which consist of a sensor histidine kinase (HK) and a response regulator (RR). In the food-borne pathogen Bacillus cereus, the alternative sigma factor sigma(B) is activated by the RR RsbY. Here we present strong indications that the PP2C-type phosphatase RsbY receives its input from the multi-sens...<br/><br/>Mark de Been, Marcel H Tempelaars, Willem van Schaik, Roy Moezelaar, Roland J Siezen, Tjakko Abee (2010) <i>Environ Microbiol</i> <i></i> <i></i> 12: 3 730-745<br/>

http://publicationslist.org/r.siezen/refid7 2010-04-30T21:41:25Z

A total of six polymorphisms were identified by comparing the genomes of the first and the last isolate of a well-characterized transmission chain of Mycobacterium tuberculosis involving five patients over a 12 and a half year period. The six polymorphisms consisted of four single nucleotide changes (SNPs), a tandem repeat polymorphism (TRP) and a previously identified IS6110 transposition event. ...<br/><br/>Anita C Schürch, Kristin Kremer, Albert Kiers, Olaf Daviena, Martin J Boeree, Roland J Siezen, Noel H Smith, Dick van Soolingen (2010) <i>Infect Genet Evol</i> <i></i> <i></i> 10: 1 108-114<br/>

http://publicationslist.org/r.siezen/refid5 2011-03-18T14:46:03Z

Lactobacillus plantarum is a ubiquitous microorganism that is able to colonize several ecological niches, including vegetables, meat, dairy substrates and the gastro-intestinal tract. An extensive phenotypic and genomic diversity analysis was conducted to elucidate the molecular basis of the high flexibility and versatility of this species. First, 185 isolates from diverse environments were phenot...<br/><br/>Roland J Siezen, Vesela A Tzeneva, Anna Castioni, Michiel Wels, Hoa T K Phan, Jan L W Rademaker, Marjo J C Starrenburg, Michiel Kleerebezem, Douwe Molenaar, Johan E T van Hylckama Vlieg (2010) <i>Environ Microbiol</i> <i></i> <i></i> 12: 3 758-773<br/>

http://publicationslist.org/r.siezen/refid4 2011-03-18T14:45:16Z

Lactic acid bacteria (LAB) are a group of gram-positive, lactic acid producing Firmicutes. They have been extensively used in food fermentations, including the production of various dairy products. The proteolytic system of LAB converts proteins to peptides and then to amino acids, which is essential for bacterial growth and also contributes significantly to flavor compounds as end-products. Recen...<br/><br/>Mengjin Liu, Jumamurat R Bayjanov, Bernadet Renckens, Arjen Nauta, Roland J Siezen (2010) <i>BMC Genomics</i> <i></i> <i></i> 11: <br/>

http://publicationslist.org/r.siezen/refid2 2011-03-18T14:45:16Z

A pangenome is the total of genes present in strains of the same species. Pangenome microarrays allow determining the genomic content of bacterial strains more accurately than conventional comparative genome hybridization microarrays. PanCGHweb is the first tool that effectively calls genotype based on pangenome microarray data. AVAILABILITY: PanCGHweb, the web tool is accessible from: http://bami...<br/><br/>Jumamurat R Bayjanov, Roland J Siezen, Sacha A F T van Hijum (2010) <i>Bioinformatics</i> <i></i> <i></i> 26: 9 1256-1257<br/>

http://publicationslist.org/r.siezen/refid3 2010-04-30T21:41:25Z

Lactobacilli belong to the lactic acid bacteria, which play a key role in industrial and artisan food raw-material fermentation, including a large variety of fermented dairy products. Next to their role in fermentation processes, specific strains of Lactobacillus are currently marketed as health-promoting cultures or probiotics. The last decade has witnessed the completion of a large number of Lac...<br/><br/>Michiel Kleerebezem, Pascal Hols, Elvis Bernard, Thomas Rolain, Miaomiao Zhou, Roland J Siezen, Peter A Bron (2010) <i>FEMS Microbiol Rev</i> <i></i> <i></i> 34: 2 199-230<br/>

http://publicationslist.org/r.siezen/refid155 2011-03-18T14:43:30Z

Rob J W Brooijmans, Roland J Siezen (2010) <i>Microb Biotechnol</i> <i></i> <i></i> 3: 5 514-522<br/>

http://publicationslist.org/r.siezen/refid1 2011-03-18T14:45:16Z

Lactococcus lactis is a lactic acid bacterium used in the production of many fermented dairy products. We report the complete genome sequence of L. lactis subsp. lactis KF147, a nondairy strain isolated from mung bean sprouts. The circular chromosome of 2,598,144 bp, the largest among the sequenced lactococcal strains, encodes many properties related to adaptation to the plant environment.<br/><br/>Roland J Siezen, Jumamurat Bayjanov, Bernadet Renckens, Michiel Wels, Sacha A F T van Hijum, Douwe Molenaar, Johan E T van Hylckama Vlieg (2010) <i>J Bacteriol</i> <i></i> <i></i> 192: 10 2649-2650<br/>

http://publicationslist.org/r.siezen/refid163 2011-03-18T14:45:16Z

Anaerobic ammonium-oxidizing (anammox) bacteria perform a key step in global nitrogen cycling. These bacteria make use of an organelle to oxidize ammonia anaerobically to nitrogen (N2) and so contribute approximately 50% of the nitrogen in the atmosphere. It is currently unknown which proteins constitute the organellar proteome and how anammox bacteria are able to specifically target organellar an...<br/><br/>Marnix H Medema, Miaomiao Zhou, Sacha A F T van Hijum, Jolein Gloerich, Hans J C T Wessels, Roland J Siezen, Marc Strous (2010) <i>BMC Genomics</i> <i></i> <i></i> 11: <br/>

http://publicationslist.org/r.siezen/refid156 2011-03-18T14:43:30Z

Roland J Siezen, Sacha A F T van Hijum (2010) <i>Microb Biotechnol</i> <i></i> <i></i> 3: 4 362-369<br/>

http://publicationslist.org/r.siezen/refid160 2011-03-18T14:45:16Z

In Lactic Acid Bacteria (LAB), the extracellular and surface-associated proteins can be involved in processes such as cell wall metabolism, degradation and uptake of nutrients, communication and binding to substrates or hosts. A genome-scale comparative study of these proteins (secretomes) can provide vast information towards the understanding of the molecular evolution, diversity, function and ad...<br/><br/>Miaomiao Zhou, Daniel Theunissen, Michiel Wels, Roland J Siezen (2010) <i>BMC Genomics</i> <i></i> <i></i> 11: <br/>

http://publicationslist.org/r.siezen/refid162 2011-03-18T14:45:16Z

To investigate whether genome sequencing yields more useful markers than those currently used to study the epidemiology of tuberculosis, it was applied to three Mycobacterium tuberculosis isolates of the Harlingen outbreak. Our findings suggest that single nucleotide polymorphisms can be used to identify transmission chains in restriction fragment length polymorphism clusters.<br/><br/>Anita C Schürch, Kristin Kremer, Olaf Daviena, Albert Kiers, Martin J Boeree, Roland J Siezen, Dick van Soolingen (2010) <i>J Clin Microbiol</i> <i></i> <i></i> 48: 9 3403-3406<br/>

http://publicationslist.org/r.siezen/refid157 2011-03-18T14:43:30Z

Roland J Siezen, Greer Wilson, Tilman Todt (2010) <i>Microb Biotechnol</i> <i></i> <i></i> 3: 2 125-130<br/>

http://publicationslist.org/r.siezen/refid158 2011-03-18T14:45:16Z

Roland J Siezen, Greer Wilson (2010) <i>Microb Biotechnol</i> <i></i> <i></i> 3: 1 1-9<br/>

http://publicationslist.org/r.siezen/refid9 2010-04-30T21:41:25Z

Carnein is an 80 kDa subtilisin-like serine protease from the latex of the plant Ipomoea carnea which displays an exceptional resistance to chemical and thermal denaturation. In order to obtain the first crystal structure of a plant subtilisin and to gain insight into the structural determinants underlying its remarkable stability, carnein was isolated from I. carnea latex, purified and crystalliz...<br/><br/>Ashok Kumar Patel, Niels van Oosterwijk, Vijay Kumar Singh, Henriëtte J Rozeboom, Kor H Kalk, Roland J Siezen, Medicherla V Jagannadham, Bauke W Dijkstra (2009) <i>Acta Crystallogr Sect F Struct Biol Cryst Commun</i> <i></i> <i></i> 65: Pt 4 383-385<br/>

http://publicationslist.org/r.siezen/refid8 2010-04-30T21:41:25Z

Lactobacillus bulgaricus and Streptococcus thermophilus, used in yogurt starter cultures, are well known for their stability and protocooperation during their coexistence in milk. In this study, we show that a close interaction between the two species also takes place at the genetic level. We performed an in silico analysis, combining gene composition and gene transfer mechanism-associated feature...<br/><br/>Mengjin Liu, Roland J Siezen, Arjen Nauta (2009) <i>Appl Environ Microbiol</i> <i></i> <i></i> 75: 12 4120-4129<br/>

http://publicationslist.org/r.siezen/refid11 2010-04-30T21:41:25Z

MOTIVATION: Pangenome arrays contain DNA oligomers targeting several sequenced reference genomes from the same species. In microbiology, these can be employed to investigate the often high genetic variability within a species by comparative genome hybridization (CGH). The biological interpretation of pangenome CGH data depends on the ability to compare strains at a functional level, particularly b...<br/><br/>Jumamurat R Bayjanov, Michiel Wels, Marjo Starrenburg, Johan E T van Hylckama Vlieg, Roland J Siezen, Douwe Molenaar (2009) <i>Bioinformatics</i> <i></i> <i></i> 25: 3 309-314<br/>

http://publicationslist.org/r.siezen/refid167 2011-03-18T14:46:04Z

Roland J Siezen, Greer Wilson (2009) <i>Microb Biotechnol</i> <i></i> <i></i> 2: 2 157-163<br/>

http://publicationslist.org/r.siezen/refid10 2010-04-30T21:41:25Z

Twenty-four Lactobacillus plantarum supermotifs (LPSMs) with lengths from approximately 800 to 1,000 nucleotides were identified in the L. plantarum genome. LPSMs were conserved in other L. plantarum strains but not in other species. Secondary structure analysis predicted that LPSMs may fold into cruciform-like structures. Preliminary experiments indicate that the LPSMs are transcribed.<br/><br/>Michiel Wels, Roger S Bongers, Jos Boekhorst, Douwe Molenaar, Mark Sturme, Willem M de Vos, Roland J Siezen, Michiel Kleerebezem (2009) <i>J Bacteriol</i> <i></i> <i></i> 191: 10 3420-3423<br/>

http://publicationslist.org/r.siezen/refid165 2011-03-18T14:46:04Z

Peter van Baarlen, Roland J Siezen (2009) <i>Microb Biotechnol</i> <i></i> <i></i> 2: 4 406-411<br/>

http://publicationslist.org/r.siezen/refid164 2011-03-18T14:46:04Z

Rob J W Brooijmans, Margreet I Pastink, Roland J Siezen (2009) <i>Microb Biotechnol</i> <i></i> <i></i> 2: 6 587-594<br/>

http://publicationslist.org/r.siezen/refid166 2011-03-18T14:46:04Z

Roland J Siezen, Greer Wilson (2009) <i>Microb Biotechnol</i> <i></i> <i></i> 2: 3 297-303<br/>

http://publicationslist.org/r.siezen/refid17 2010-04-30T21:41:25Z

BACKGROUND: In the past decades, various protein subcellular-location (SCL) predictors have been developed. Most of these predictors, like TMHMM 2.0, SignalP 3.0, PrediSi and Phobius, aim at the identification of one or a few SCLs, whereas others such as CELLO and Psortb.v.2.0 aim at a broader classification. Although these tools and pipelines can achieve a high precision in the accurate predictio...<br/><br/>Miaomiao Zhou, Jos Boekhorst, Christof Francke, Roland J Siezen (2008) <i>BMC Bioinformatics</i> <i></i> <i></i> 9: <br/>

http://publicationslist.org/r.siezen/refid16 2010-04-30T21:41:25Z

Noroviruses (NoVs) are considered to be a major cause of acute nonbacterial gastroenteritis in humans. The NoV genus is genetically diverse, and genotype GII.4 has been most commonly identified worldwide in recent years. In this study we analyzed the complete capsid gene of NoV strains belonging to the less prevalent genotype GII.2. We compared a total of 36 complete capsid sequences of GII.2 sequ...<br/><br/>Nobuhiro Iritani, Harry Vennema, J Joukje Siebenga, Roland J Siezen, Bernadet Renckens, Yoshiyuki Seto, Atsushi Kaida, Marion Koopmans (2008) <i>J Virol</i> <i></i> <i></i> 82: 15 7336-7345<br/>

http://publicationslist.org/r.siezen/refid18 2010-04-30T21:41:25Z

BACKGROUND: A key problem in the sequence-based reconstruction of regulatory networks in bacteria is the lack of specificity in operator predictions. The problem is especially prominent in the identification of transcription factor (TF) specific binding sites. More in particular, homologous TFs are abundant and, as they are structurally very similar, it proves difficult to distinguish the related ...<br/><br/>Christof Francke, Robert Kerkhoven, Michiel Wels, Roland J Siezen (2008) <i>BMC Genomics</i> <i></i> <i></i> 9: <br/>

http://publicationslist.org/r.siezen/refid19 2010-04-30T21:41:25Z

To what extent can modes of gene regulation be explained by systems-level properties of metabolic networks? Prior studies on co-regulation of metabolic genes have mainly focused on graph-theoretical features of metabolic networks and demonstrated a decreasing level of co-expression with increasing network distance, a naïve, but widely used, topological index. Others have suggested that static gra...<br/><br/>Richard A Notebaart, Bas Teusink, Roland J Siezen, Balázs Papp (2008) <i>PLoS Comput Biol</i> <i></i> <i></i> 4: 1 <br/>

http://publicationslist.org/r.siezen/refid172 2011-03-18T14:47:13Z

Roland J Siezen (2008) <i>Microb Biotechnol</i> <i></i> <i></i> 1: 2 97-103<br/>

http://publicationslist.org/r.siezen/refid22 2010-04-30T21:41:25Z

Lactococcus lactis is a primary constituent of many starter cultures used for the manufacturing of fermented dairy products, but the species also occurs in various nondairy niches such as (fermented) plant material. Three genome sequences of L. lactis dairy strains (IL-1403, SK11, and MG1363) are publicly available. An extensive molecular and phenotypic diversity analysis was now performed on two ...<br/><br/>Roland J Siezen, Marjo J C Starrenburg, Jos Boekhorst, Bernadet Renckens, Douwe Molenaar, Johan E T van Hylckama Vlieg (2008) <i>Appl Environ Microbiol</i> <i></i> <i></i> 74: 2 424-436<br/>

http://publicationslist.org/r.siezen/refid20 2010-04-30T21:41:25Z

Microarrays are used to profile transcriptional activity, providing global cell biology insight. Particularly for plants, interpretation of transcriptional profiles is challenging because many genes have unknown functions. Furthermore, many plant gene sequences do not have clear homologs in other model organisms. Fortunately, over the past five years, various tools that assist plant scientists hav...<br/><br/>Peter van Baarlen, H Peter van Esse, Roland J Siezen, Bart P H J Thomma (2008) <i>Trends Plant Sci</i> <i></i> <i></i> 13: 1 44-50<br/>

http://publicationslist.org/r.siezen/refid168 2011-03-18T14:46:33Z

Roland J Siezen, Herwig Bachmann (2008) <i>Microb Biotechnol</i> <i></i> <i></i> 1: 6 435-442<br/>

http://publicationslist.org/r.siezen/refid15 2010-04-30T21:41:25Z

Mengjin Liu, Arjen Nauta, Christof Francke, Roland J Siezen (2008) <i>Appl Environ Microbiol</i> <i></i> <i></i> 74: 15 4590-4600<br/>

http://publicationslist.org/r.siezen/refid14 2010-04-30T21:41:25Z

BACKGROUND: T-box anti-termination is an elegant and sensitive mechanism by which many bacteria maintain constant levels of amino acid-charged tRNAs. The amino acid specificity of the regulatory element is related to a so-called specifier codon and can in principle be used to guide the functional annotation of the genes controlled via the T-box anti-termination mechanism. RESULTS: Hidden Markov Mo...<br/><br/>Michiel Wels, Tom Groot Kormelink, Michiel Kleerebezem, Roland J Siezen, Christof Francke (2008) <i>BMC Genomics</i> <i></i> <i></i> 9: <br/>

http://publicationslist.org/r.siezen/refid170 2011-03-18T14:46:33Z

Roland J Siezen, Barzan I Khayatt (2008) <i>Microb Biotechnol</i> <i></i> <i></i> 1: 4 275-282<br/>

http://publicationslist.org/r.siezen/refid171 2011-03-18T14:46:33Z

Roland J Siezen, Greer Wilson (2008) <i>Microb Biotechnol</i> <i></i> <i></i> 1: 3 202-207<br/>

http://publicationslist.org/r.siezen/refid169 2011-03-18T14:46:33Z

Roland J Siezen, Marco Galardini (2008) <i>Microb Biotechnol</i> <i></i> <i></i> 1: 5 333-340<br/>

http://publicationslist.org/r.siezen/refid13 2010-04-30T21:41:25Z

In bacteria, environmental challenges are often translated into a transcriptional response via the cognate response regulators (RRs) of specialized two-component systems (TCSs). A phylogenetic footprinting/shadowing approach was designed and used to identify many novel RR-specific operators for species of the Bacillus cereus group and related Gram-positives. Analysis of the operator sequences reve...<br/><br/>Mark de Been, Marieke J Bart, Tjakko Abee, Roland J Siezen, Christof Francke (2008) <i>Environ Microbiol</i> <i></i> <i></i> 10: 10 2796-2809<br/>

http://publicationslist.org/r.siezen/refid12 2010-04-30T21:41:25Z

Most Gram-positive bacteria inhabiting the gastrointestinal tract are capable of hydrolysing bile salts. Bile salt hydrolysis is thought to play an important role in various biological processes in the host. Therefore, correct annotation of bacterial bile salt hydrolases (Bsh) in public databases (EC 3.5.1.24) is of importance, especially for lactobacilli, which are considered to play a major role...<br/><br/>Jolanda M Lambert, Roland J Siezen, Willem M de Vos, Michiel Kleerebezem (2008) <i>Microbiology</i> <i></i> <i></i> 154: Pt 8 2492-2500<br/>

http://publicationslist.org/r.siezen/refid24 2010-04-30T21:41:25Z

Subtilisin-like serine proteases (subtilases) are a very diverse family of serine proteases with low sequence homology, often limited to regions surrounding the three catalytic residues. Starting with different Hidden Markov Models (HMM), based on sequence alignments around the catalytic residues of the S8 family (subtilisins) and S53 family (sedolisins), we iteratively searched all ORFs in the co...<br/><br/>Roland J Siezen, Bernadet Renckens, Jos Boekhorst (2007) <i>Proteins</i> <i></i> <i></i> 67: 3 681-694<br/>

http://publicationslist.org/r.siezen/refid21 2010-04-30T21:41:25Z

In silico identification criteria were defined to predict if genes encoding histidine protein kinases (HPKs) and response regulators (RRs) could be part of peptide-based quorum sensing (QS) two-component regulatory systems (QS-TCSs) in Firmicutes. These criteria were used to screen HPKs and RRs annotated on the completed genome sequences of Lactobacillus species, and several (putative) QS-TCSs wer...<br/><br/>Mark H J Sturme, Christof Francke, Roland J Siezen, Willem M de Vos, Michiel Kleerebezem (2007) <i>Microbiology</i> <i></i> <i></i> 153: Pt 12 3939-3947<br/>

http://publicationslist.org/r.siezen/refid23 2010-04-30T21:41:25Z

Noroviruses are the causative agents of the majority of viral gastroenteritis outbreaks in humans. During the past 15 years, noroviruses of genotype GGII.4 have caused four epidemic seasons of viral gastroenteritis, during which four novel variants (termed epidemic variants) emerged and displaced the resident viruses. In order to understand the mechanisms and biological advantages of these epidemi...<br/><br/>J Joukje Siebenga, Harry Vennema, Bernadet Renckens, Erwin de Bruin, Bas van der Veer, Roland J Siezen, Marion Koopmans (2007) <i>J Virol</i> <i></i> <i></i> 81: 18 9932-9941<br/>

http://publicationslist.org/r.siezen/refid31 2010-04-30T21:41:25Z

Lactic acid bacteria (LAB) are frequently encountered inhabitants of the human intestinal tract. A protective layer of mucus covers the epithelial cells of the intestine, offering an attachment site for these bacteria. In this study bioinformatics tools were used to identify and characterize proteins containing one type of mucus-binding domain, called MUB, that is postulated to play an important r...<br/><br/>Jos Boekhorst, Quinta Helmer, Michiel Kleerebezem, Roland J Siezen (2006) <i>Microbiology</i> <i></i> <i></i> 152: Pt 1 273-280<br/>

http://publicationslist.org/r.siezen/refid30 2010-04-30T21:41:25Z

Lactococcus lactis is the primary model organism for lactic acid bacteria (LAB) and is widely used in the production of fermented dairy products. In recent years there has been increasing interest in strains isolated from non-dairy environments, as these exhibit a high metabolic diversity and have unique flavour-forming activities. Recent progress has been made in understanding the natural diversi...<br/><br/>Johan E T van Hylckama Vlieg, Jan L W Rademaker, Herwig Bachmann, Douwe Molenaar, William J Kelly, Roland J Siezen (2006) <i>Curr Opin Biotechnol</i> <i></i> <i></i> 17: 2 183-190<br/>

http://publicationslist.org/r.siezen/refid33 2010-04-30T21:41:25Z

The complete genome sequences of the lactic acid bacteria (LAB), Lactobacillus plantarum, Lactococcus lactis, and Lactobacillus johnsonii were used to compare location, sequence, organisation, and regulation of the ribosomal RNA (rrn) operons. All rrn operons of the examined LAB diverge from the origin of replication, which is compatible with their efficient expression. All operons show a common o...<br/><br/>Maaike C de Vries, Roland J Siezen, Janneke G E Wijman, Yuan Zhao, Michiel Kleerebezem, Willem M de Vos, Elaine E Vaughan (2006) <i>Syst Appl Microbiol</i> <i></i> <i></i> 29: 5 358-367<br/>

http://publicationslist.org/r.siezen/refid29 2010-04-30T21:41:25Z

Cis-acting elements in Lactobacillus plantarum were predicted by comparative analysis of the upstream regions of conserved genes and predicted transcriptional units (TUs) in different bacterial genomes. TUs were predicted for two species sets, with different evolutionary distances to L.plantarum. TUs were designated 'cluster of orthologous transcriptional units' (COT) when >50% of the genes were o...<br/><br/>Michiel Wels, Christof Francke, Robert Kerkhoven, Michiel Kleerebezem, Roland J Siezen (2006) <i>Nucleic Acids Res</i> <i></i> <i></i> 34: 7 1947-1958<br/>

http://publicationslist.org/r.siezen/refid26 2010-04-30T21:41:25Z

A genome-scale metabolic model of the lactic acid bacterium Lactobacillus plantarum WCFS1 was constructed based on genomic content and experimental data. The complete model includes 721 genes, 643 reactions, and 531 metabolites. Different stoichiometric modeling techniques were used for interpretation of complex fermentation data, as L. plantarum is adapted to nutrient-rich environments and only g...<br/><br/>Bas Teusink, Anne Wiersma, Douwe Molenaar, Christof Francke, Willem M de Vos, Roland J Siezen, Eddy J Smid (2006) <i>J Biol Chem</i> <i></i> <i></i> 281: 52 40041-40048<br/>

http://publicationslist.org/r.siezen/refid27 2010-04-30T21:41:25Z

Members of the Bacillus cereus group are ubiquitously present in the environment and can adapt to a wide range of environmental fluctuations. In bacteria, these adaptive responses are generally mediated by two-component signal transduction systems (TCSs), which consist of a histidine kinase (HK) and its cognate response regulator (RR). With the use of in silico techniques, a complete set of HKs an...<br/><br/>Mark de Been, Christof Francke, Roy Moezelaar, Tjakko Abee, Roland J Siezen (2006) <i>Microbiology</i> <i></i> <i></i> 152: Pt 10 3035-3048<br/>

http://publicationslist.org/r.siezen/refid25 2010-04-30T21:41:25Z

The predicted extracellular proteins of the bacterium Lactobacillus plantarum were analysed to gain insight into the mechanisms underlying interactions of this bacterium with its environment. Extracellular proteins play important roles in processes ranging from probiotic effects in the gastrointestinal tract to degradation of complex extracellular carbon sources such as those found in plant materi...<br/><br/>Jos Boekhorst, Michiel Wels, Michiel Kleerebezem, Roland J Siezen (2006) <i>Microbiology</i> <i></i> <i></i> 152: Pt 11 3175-3183<br/>

http://publicationslist.org/r.siezen/refid28 2010-04-30T21:41:25Z

BACKGROUND: The genomic information of a species allows for the genome-scale reconstruction of its metabolic capacity. Such a metabolic reconstruction gives support to metabolic engineering, but also to integrative bioinformatics and visualization. Sequence-based automatic reconstructions require extensive manual curation, which can be very time-consuming. Therefore, we present a method to acceler...<br/><br/>Richard A Notebaart, Frank H J van Enckevort, Christof Francke, Roland J Siezen, Bas Teusink (2006) <i>BMC Bioinformatics</i> <i></i> <i></i> 7: <br/>

http://publicationslist.org/r.siezen/refid38 2010-04-30T21:41:25Z

Lactobacillus plantarum is a versatile and flexible species that is encountered in a variety of niches and can utilize a broad range of fermentable carbon sources. To assess if this versatility is linked to a variable gene pool, microarrays containing a subset of small genomic fragments of L. plantarum strain WCFS1 were used to perform stringent genotyping of 20 strains of L. plantarum from variou...<br/><br/>Douwe Molenaar, Françoise Bringel, Frank H Schuren, Willem M de Vos, Roland J Siezen, Michiel Kleerebezem (2005) <i>J Bacteriol</i> <i></i> <i></i> 187: 17 6119-6127<br/>

http://publicationslist.org/r.siezen/refid39 2010-04-30T21:41:25Z

Surface proteins of gram-positive bacteria often play a role in adherence of the bacteria to host tissue and are frequently required for virulence. A specific subgroup of extracellular proteins contains the cell wall-sorting motif LPxTG, which is the target for cleavage and covalent coupling to the peptidoglycan by enzymes called sortases. A comprehensive set of putative sortase substrates was ide...<br/><br/>Jos Boekhorst, Mark W H J de Been, Michiel Kleerebezem, Roland J Siezen (2005) <i>J Bacteriol</i> <i></i> <i></i> 187: 14 4928-4934<br/>

http://publicationslist.org/r.siezen/refid40 2010-04-30T21:41:25Z

E J Smid, F J H van Enckevort, A Wegkamp, J Boekhorst, D Molenaar, J Hugenholtz, R J Siezen, B Teusink (2005) <i>J Appl Microbiol</i> <i></i> <i></i> 98: 6 1326-1331<br/>

http://publicationslist.org/r.siezen/refid37 2010-04-30T21:41:25Z

The prospect of understanding the relationship between the genome and the physiology of an organism is an important incentive to reconstruct metabolic networks. The first steps in the process can be automated and it does not take much effort to obtain an initial metabolic reconstruction from a genome sequence. However, such a reconstruction is certainly not flawless and correction of the many impe...<br/><br/>Christof Francke, Roland J Siezen, Bas Teusink (2005) <i>Trends Microbiol</i> <i></i> <i></i> 13: 11 550-558<br/>

http://publicationslist.org/r.siezen/refid41 2010-04-30T21:41:25Z

Lactobacillus plantarum WCFS1 harbors three plasmids, pWCFS101, pWCFS102, and pWCFS103, with sizes of 1,917, 2,365, and 36,069 bp, respectively. The two smaller plasmids are of unknown function and contain replication genes that are likely to function via the rolling-circle replication mechanism. The host range of the pWCFS101 replicon includes Lactobacillus species and Lactococcus lactis, while t...<br/><br/>Richard van Kranenburg, Natasa Golic, Roger Bongers, Rob J Leer, Willem M de Vos, Roland J Siezen, Michiel Kleerebezem (2005) <i>Appl Environ Microbiol</i> <i></i> <i></i> 71: 3 1223-1230<br/>

http://publicationslist.org/r.siezen/refid36 2010-04-30T21:41:25Z

A key complication in comparative genomics for reliable gene function prediction is the existence of duplicated genes. To study the effect of gene duplication on function prediction, we analyze orthologs between pairs of genomes where in one genome the orthologous gene has duplicated after the speciation of the two genomes (i.e. inparalogs). For these duplicated genes we investigate whether the ge...<br/><br/>Richard A Notebaart, Martijn A Huynen, Bas Teusink, Roland J Siezen, Berend Snel (2005) <i>Nucleic Acids Res</i> <i></i> <i></i> 33: 19 6164-6171<br/>

http://publicationslist.org/r.siezen/refid32 2010-04-30T21:41:25Z

Mengjin Liu, Frank H J van Enckevort, Roland J Siezen (2005) <i>Microbiology</i> <i></i> <i></i> 151: Pt 12 3811-3814<br/>

http://publicationslist.org/r.siezen/refid34 2010-04-30T21:41:25Z

Lactococcus lactis strains are known to carry plasmids encoding industrially important traits. L. lactis subsp. cremoris SK11 is widely used by the dairy industry in cheese making. Its complete plasmid complement was sequenced and found to contain the plasmids pSK11A (10,372 bp), pSK11B (13,332 bp), pSK11L (47,165 bp), and pSK11P (75,814 bp). Six highly homologous repB-containing replicons were fo...<br/><br/>Roland J Siezen, Bernadet Renckens, Iris van Swam, Sander Peters, Richard van Kranenburg, Michiel Kleerebezem, Willem M de Vos (2005) <i>Appl Environ Microbiol</i> <i></i> <i></i> 71: 12 8371-8382<br/>

http://publicationslist.org/r.siezen/refid35 2010-04-30T21:41:25Z

On the basis of the annotated genome we reconstructed the metabolic pathways of the lactic acid bacterium Lactobacillus plantarum WCFS1. After automatic reconstruction by the Pathologic tool of Pathway Tools (http://bioinformatics.ai.sri.com/ptools/), the resulting pathway-genome database, LacplantCyc, was manually curated extensively. The current database contains refinements to existing routes a...<br/><br/>Bas Teusink, Frank H J van Enckevort, Christof Francke, Anne Wiersma, Arno Wegkamp, Eddy J Smid, Roland J Siezen (2005) <i>Appl Environ Microbiol</i> <i></i> <i></i> 71: 11 7253-7262<br/>

http://publicationslist.org/r.siezen/refid45 2010-04-30T21:41:25Z

SUMMARY: A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a MySQL database. The generated images are in scalable vector graphics (SVG) format, which is suitable f...<br/><br/>Robert Kerkhoven, Frank H J van Enckevort, Jos Boekhorst, Douwe Molenaar, Roland J Siezen (2004) <i>Bioinformatics</i> <i></i> <i></i> 20: 11 1812-1814<br/>

http://publicationslist.org/r.siezen/refid44 2010-04-30T21:41:25Z

Lactic acid bacteria (LAB) have been widely used in food fermentations and, more recently, as probiotics in health-promoting food products. Genome sequencing and functional genomics studies of a variety of LAB are now rapidly providing insights into their diversity and evolution and revealing the molecular basis for important traits such as flavor formation, sugar metabolism, stress response, adap...<br/><br/>Roland J Siezen, Frank H J van Enckevort, Michiel Kleerebezem, Bas Teusink (2004) <i>Curr Opin Biotechnol</i> <i></i> <i></i> 15: 2 105-115<br/>

http://publicationslist.org/r.siezen/refid42 2010-04-30T21:41:25Z

Genome sequences are now available for many of the microbes that cause food-borne diseases. The information contained in pathogen genome sequences, together with the development of themed and whole-genome DNA microarrays and improved proteomics techniques, might provide tools for the rapid detection and identification of such organisms, for assessing their biological diversity and for understandin...<br/><br/>Tjakko Abee, Willem van Schaik, Roland J Siezen (2004) <i>Trends Biotechnol</i> <i></i> <i></i> 22: 12 653-660<br/>

http://publicationslist.org/r.siezen/refid43 2010-04-30T21:41:25Z

The first comprehensive comparative analysis of lactobacilli was done by comparing the genomes of Lactobacillus plantarum (3.3 Mb) and Lactobacillus johnsonii (2.0 Mb). L. johnsonii is predominantly found in the gastrointestinal tract, while L. plantarum is also found on plants and plant-derived material, and is used in a variety of industrial fermentations. The L. plantarum and L. johnsonii chrom...<br/><br/>Jos Boekhorst, Roland J Siezen, Marie-Camille Zwahlen, David Vilanova, Raymond D Pridmore, Annick Mercenier, Michiel Kleerebezem, Willem M de Vos, Harald Brüssow, Frank Desiere (2004) <i>Microbiology</i> <i></i> <i></i> 150: Pt 11 3601-3611<br/>

http://publicationslist.org/r.siezen/refid47 2010-04-30T21:41:25Z

The 3,308,274-bp sequence of the chromosome of Lactobacillus plantarum strain WCFS1, a single colony isolate of strain NCIMB8826 that was originally isolated from human saliva, has been determined, and contains 3,052 predicted protein-encoding genes. Putative biological functions could be assigned to 2,120 (70%) of the predicted proteins. Consistent with the classification of L. plantarum as a fac...<br/><br/>Michiel Kleerebezem, Jos Boekhorst, Richard van Kranenburg, Douwe Molenaar, Oscar P Kuipers, Rob Leer, Renato Tarchini, Sander A Peters, Hans M Sandbrink, Mark W E J Fiers, Willem Stiekema, René M Klein Lankhorst, Peter A Bron, Sally M Hoffer, Masja N Nierop Groot, Robert Kerkhoven, Maaike de Vries, Björn Ursing, Willem M de Vos, Roland J Siezen (2003) <i>Proc Natl Acad Sci U S A</i> <i></i> <i></i> 100: 4 1990-1995<br/>

http://publicationslist.org/r.siezen/refid46 2010-04-30T21:41:25Z

The Lactobacillus plantarum commensal WCFS1 contains four prophage elements in its genome. Lp1 and Lp2 are two about 40-kb-long uninducible prophages that share closely related DNA packaging, head and tail genes defining a second lineage of pac-site Siphoviridae in L. plantarum, distinct from L. plantarum phage phig1e, but related to Bacillus phage SPP1 and Lactococcus phage TP901-1. Northern anal...<br/><br/>Marco Ventura, Carlos Canchaya, Michiel Kleerebezem, Willem M de Vos, Roland J Siezen, Harald Brüssow (2003) <i>Virology</i> <i></i> <i></i> 316: 2 245-255<br/>

http://publicationslist.org/r.siezen/refid52 2010-04-30T21:41:25Z

Sulfur metabolism in gram-positive bacteria is poorly characterized. Information on the molecular mechanisms of regulation of genes involved in sulfur metabolism is limited, and no regulator genes have been identified. Here we describe the regulation of the lactococcal metC-cysK operon, encoding a cystathionine beta-lyase (metC) and cysteine synthase (cysK). Its expression was shown to be negative...<br/><br/>María Fernández, Michiel Kleerebezem, Oscar P Kuipers, Roland J Siezen, Richard van Kranenburg (2002) <i>J Bacteriol</i> <i></i> <i></i> 184: 1 82-90<br/>

http://publicationslist.org/r.siezen/refid48 2010-04-30T21:41:25Z

R J Siezen, J Kok, T Abee, G Schaafsma (2002) <i>Antonie Van Leeuwenhoek</i> <i></i> <i></i> 82: 1-4 <br/>

http://publicationslist.org/r.siezen/refid51 2010-04-30T21:41:25Z

EXProt is a non-redundant protein database containing a selection of entries from genome annotation projects and public databases, aimed at including only proteins with an experimentally verified function. In EXProt release 2.0 we have collected entries from the Pseudomonas aeruginosa community annotation project (PseudoCAP), the Escherichia coli genome and proteome database (GenProtEC) and the tr...<br/><br/>Björn M Ursing, Frank H J van Enckevort, Jack A M Leunissen, Roland J Siezen (2002) <i>Nucleic Acids Res</i> <i></i> <i></i> 30: 1 50-51<br/>

http://publicationslist.org/r.siezen/refid50 2010-04-30T21:41:25Z

EXProt (database for EXPerimentally verified Protein functions) is a new non-redundant database containing protein sequences for which the function has been experimentally verified. It is a selection of 3976 entries from the Prokaryotes section of the EMBL Nucleotide Sequence Database, Release 66, and 375 entries from the Pseudomonas Community Annotation Project (PseudoCAP). The entries in EXProt ...<br/><br/>Björn M Ursing, Frank H J van Enckevort, Jack A M Leunissen, Roland J Siezen (2002) <i>In Silico Biol</i> <i></i> <i></i> 2: 1 1-4<br/>

http://publicationslist.org/r.siezen/refid49 2010-04-30T21:41:25Z

The fls gene encoding fervidolysin, a keratin-degrading proteolytic enzyme from the thermophilic bacterium Fervidobacterium pennivorans, was isolated using degenerate primers combined with Southern hybridization and inverse polymerase chain reaction. Further sequence characterization demonstrated that the 2.1-kb fls gene encoded a 699-amino-acid preproenzyme showing high homology with the subtilis...<br/><br/>Leon D Kluskens, Wilfried G B Voorhorst, Roland J Siezen, Ruth M Schwerdtfeger, Garabed Antranikian, John van der Oost, Willem M de Vos (2002) <i>Extremophiles</i> <i></i> <i></i> 6: 3 185-194<br/>

http://publicationslist.org/r.siezen/refid54 2010-04-30T21:41:25Z

W M de Vos, W G Voorhorst, M Dijkgraaf, L D Kluskens, J Van der Oost, R J Siezen (2001) <i>Methods Enzymol</i> <i></i> <i></i> 330: 383-393<br/>

http://publicationslist.org/r.siezen/refid53 2010-04-30T21:41:25Z

BACKGROUND: The genome of Mycobacterium tuberculosis H37Rv has five copies of a cluster of genes known as the ESAT-6 loci. These clusters contain members of the CFP-10 (lhp) and ESAT-6 (esat-6) gene families (encoding secreted T-cell antigens that lack detectable secretion signals) as well as genes encoding secreted, cell-wall-associated subtilisin-like serine proteases, putative ABC transporters,...<br/><br/>N C Gey Van Pittius, J Gamieldien, W Hide, G D Brown, R J Siezen, A D Beyers (2001) <i>Genome Biol</i> <i></i> <i></i> 2: 10 <br/>

http://publicationslist.org/r.siezen/refid56 2010-04-30T21:41:25Z

The gene encoding the major intracellular tributyrin esterase of Lactococcus lactis was cloned using degenerate DNA probes based on 19 known N-terminal amino acid residues of the purified enzyme. The gene, named estA, was sequenced and found to encode a protein of 258 amino acid residues. The transcription start site was mapped 233 nucleotides upstream of the start codon, and a canonical promoter ...<br/><br/>L Fernández, M M Beerthuyzen, J Brown, R J Siezen, T Coolbear, R Holland, O P Kuipers (2000) <i>Appl Environ Microbiol</i> <i></i> <i></i> 66: 4 1360-1368<br/>

http://publicationslist.org/r.siezen/refid55 2010-04-30T21:41:25Z

The Lactococcus lactis SK11 cell envelope proteinase is an extracellular, multidomain protein of nearly 2,000 residues consisting of an N-terminal serine protease domain, followed by various other domains of largely unknown function. Using a strategy of deletion mutagenesis, we have analyzed the function of several C-terminal domains of the SK11 proteinase which are absent in cell envelope protein...<br/><br/>P G Bruinenberg, W M De Vos, R J Siezen (2000) <i>Appl Environ Microbiol</i> <i></i> <i></i> 66: 7 2859-2865<br/>

http://publicationslist.org/r.siezen/refid58 2010-04-30T21:41:25Z

The multi-domain, cell-envelope proteinases encoded by the genes prtB of Lactobacillus delbrueckii subsp. bulgaricus, prtH of Lactobacillus helveticus, prtP of Lactococcus lactis, scpA of Streptococcus pyogenes and csp of Streptococcus agalactiae have been compared using multiple sequence alignment, secondary structure prediction and database homology searching methods. This comparative analysis h...<br/><br/>R J Siezen (1999) <i>Antonie Van Leeuwenhoek</i> <i></i> <i></i> 76: 1-4 139-155<br/>

http://publicationslist.org/r.siezen/refid57 2010-04-30T21:41:25Z

C van Kraaij, W M de Vos, R J Siezen, O P Kuipers (1999) <i>Nat Prod Rep</i> <i></i> <i></i> 16: 5 575-587<br/>

http://publicationslist.org/r.siezen/refid60 2010-04-30T21:41:25Z

Nisin is a 34 residue long peptide belonging to the group A lantibiotics with antimicrobial activity against Gram-positive bacteria. The antimicrobial activity is based on pore formation in the cytoplasmic membrane of target organisms. The mechanism which leads to pore formation remains to be clarified. We studied the orientation of nisin via site-directed tryptophan fluorescence spectroscopy. The...<br/><br/>E Breukink, C van Kraaij, A van Dalen, R A Demel, R J Siezen, B de Kruijff, O P Kuipers (1998) <i>Biochemistry</i> <i></i> <i></i> 37: 22 8153-8162<br/>

http://publicationslist.org/r.siezen/refid59 2010-04-30T21:41:25Z

Nisin is an amphiphilic peptide with a strong antimicrobial activity against various Gram-positive bacteria. Its activity results from permeabilization of bacterial membranes, causing efflux of cytoplasmic compounds. To get information on the molecular mechanism of membrane permeabilization, a mutant of nisin Z containing the C-terminal extension Asp-(His)6 was produced. The biological and anionic...<br/><br/>C van Kraaij, E Breukink, M A Noordermeer, R A Demel, R J Siezen, O P Kuipers, B de Kruijff (1998) <i>Biochemistry</i> <i></i> <i></i> 37: 46 16033-16040<br/>

http://publicationslist.org/r.siezen/refid64 2010-04-30T21:41:25Z

The interaction of nisin Z and a nisin Z mutant carrying a negative charge in the C-terminus ([Glu-32]-nisin Z) with anionic lipids was characterized in model membrane systems, and bacterial membrane systems. We focused on three possible steps in the mode of action of nisin, i.e., binding, insertion, and pore formation of nisin Z. Increasing amounts of anionic lipids in both model and natural memb...<br/><br/>E Breukink, C van Kraaij, R A Demel, R J Siezen, O P Kuipers, B de Kruijff (1997) <i>Biochemistry</i> <i></i> <i></i> 36: 23 6968-6976<br/>

http://publicationslist.org/r.siezen/refid63 2010-04-30T21:41:25Z

Three mutants of the antibiotic nisin Z, in which the Val32 residue was replaced by a Glu, Lys or Trp residue, were produced and characterized for the purpose of establishing the role of charge differences in the C-terminal part of nisin on antimicrobial activity and signaling properties. 1H-NMR analyses showed that all three mutants harbor an unmodified serine residue at position 33, instead of t...<br/><br/>C Van Kraaij, E Breukink, H S Rollema, R J Siezen, R A Demel, B De Kruijff, O P Kuipers (1997) <i>Eur J Biochem</i> <i></i> <i></i> 247: 1 114-120<br/>

http://publicationslist.org/r.siezen/refid65 2010-04-30T21:41:25Z

Subtilases are members of the clan (or superfamily) of subtilisin-like serine proteases. Over 200 subtilases are presently known, more than 170 of which with their complete amino acid sequence. In this update of our previous overview (Siezen RJ, de Vos WM, Leunissen JAM, Dijkstra BW, 1991, Protein Eng 4:719-731), details of more than 100 new subtilases discovered in the past five years are summari...<br/><br/>R J Siezen, J A Leunissen (1997) <i>Protein Sci</i> <i></i> <i></i> 6: 3 501-523<br/>

http://publicationslist.org/r.siezen/refid62 2010-04-30T21:41:25Z

The hyperthermophilic archaeon Pyrococcus furiosus produces an extracellular, glycosylated hyperthermostable subtilisin-like serine protease, termed pyrolysin (Voorhorst,W.G.B., Eggen,R.I.L., Geerling,A.C.M., Platteeuw,C., Siezen,R.J. and de Vos,W.M. (1996) J. Biol. Chem., 271, 20426-20431). Based on the pyrolysin coding sequence, a pyrolysin-like gene fragment was cloned and characterized from th...<br/><br/>W G Voorhorst, A Warner, W M de Vos, R J Siezen (1997) <i>Protein Eng</i> <i></i> <i></i> 10: 8 905-914<br/>

http://publicationslist.org/r.siezen/refid61 2010-04-30T21:41:25Z

The antimicrobial membrane-interacting polypeptide nisin is a prominent member of the lantibiotic family, the members of which contain thioether-bridged residues called lanthionines. To gain insight into the complex biosynthesis and the structure/function relationship of lantibiotics, the final intermediate in the biosynthesis of nisin A was studied by nuclear magnetic resonance spectroscopy. In a...<br/><br/>H W van den Hooven, H S Rollema, R J Siezen, C W Hilbers, O P Kuipers (1997) <i>Biochemistry</i> <i></i> <i></i> 36: 46 14137-14145<br/>

http://publicationslist.org/r.siezen/refid71 2010-04-30T21:41:25Z

Whereas protein engineering of enzymes and structural proteins nowadays is an established research tool for studying structure-function relationships of polypeptides and for improving their properties, the engineering of posttranslationally modified peptides, such as the lantibiotics, is just coming of age. The engineering of lantibiotics is less straightforward than that of unmodified proteins, s...<br/><br/>O P Kuipers, G Bierbaum, B Ottenwälder, H M Dodd, N Horn, J Metzger, T Kupke, V Gnau, R Bongers, P van den Bogaard, H Kosters, H S Rollema, W M de Vos, R J Siezen, G Jung, F Götz, H G Sahl, M J Gasson (1996) <i>Antonie Van Leeuwenhoek</i> <i></i> <i></i> 69: 2 161-169<br/>

http://publicationslist.org/r.siezen/refid72 2010-04-30T21:41:25Z

Monomolecular layers of lipids at the air/water interface have been used as a model membrane to study membrane interactions of the lantibiotic nisin. The natural lantibiotics nisin A and nisin Z proved to have a high affinity for the anionic lipids phosphatidylglycerol and bis(phosphatidyl)glycerol (cardiolipin). The interaction with zwitterionic phopholipids or neutral lipids is very low at surfa...<br/><br/>R A Demel, T Peelen, R J Siezen, B De Kruijff, O P Kuipers (1996) <i>Eur J Biochem</i> <i></i> <i></i> 235: 1-2 267-274<br/>

http://publicationslist.org/r.siezen/refid74 2010-04-30T21:41:25Z

Homology modelling was used to predict enzyme-substrate interactions in three entirely different subtilisin-like enzymes of unknown three-dimensional structure. i.e. (a) cell-envelope proteinase of Lactococcus lactis, (b) putative leader peptidase for pre-nisin from L. lactis, and (c) human furin. Models were based on known three-dimensional structures of subtilisins and thermitase in complex with...<br/><br/>R J Siezen (1996) <i>Adv Exp Med Biol</i> <i></i> <i></i> 379: 63-73<br/>

http://publicationslist.org/r.siezen/refid70 2010-04-30T21:41:25Z

Lantibiotics form a group of modified peptides with unique structures, containing post-translationally modified amino acids such as dehydrated and lanthionine residues. In the gram-positive bacteria that secrete these lantibiotics, the gene clusters flanking the structural genes for various linear (type A) lantibiotics have recently been characterized. The best studied representatives are those of...<br/><br/>R J Siezen, O P Kuipers, W M de Vos (1996) <i>Antonie Van Leeuwenhoek</i> <i></i> <i></i> 69: 2 171-184<br/>

http://publicationslist.org/r.siezen/refid69 2010-04-30T21:41:25Z

The lantibiotic lacticin 481 is a bacteriocin produced by Lactococcus lactis ssp. lactis. This polypeptide contains 27 amino acids, including the unusual residues dehydrobutyrine and the thioether-bridging lanthionine and 3-methyllanthionine. Lacticin 481 belongs to a structurally distinct group of lantibiotics, which also include streptococcin A-FF22, salivaricin A and variacin. Here we report th...<br/><br/>H W van den Hooven, F M Lagerwerf, W Heerma, J Haverkamp, J C Piard, C W Hilbers, R J Siezen, O P Kuipers, H S Rollema (1996) <i>FEBS Lett</i> <i></i> <i></i> 391: 3 317-322<br/>

http://publicationslist.org/r.siezen/refid67 2010-04-30T21:41:25Z

Clinical isolates of Enterococcus faecalis more commonly produce a cytolysin than do commensal isolates. Epidemiologic evidence and animal-model studies have established a role for the cytolysin in the pathogenesis of enterococcal disease. The cytolysin consists of two structural subunits, CylLL and CylLS, that are activated by a third component, CylA. Genetic and biochemical characterization of C...<br/><br/>M C Booth, C P Bogie, H G Sahl, R J Siezen, K L Hatter, M S Gilmore (1996) <i>Mol Microbiol</i> <i></i> <i></i> 21: 6 1175-1184<br/>

http://publicationslist.org/r.siezen/refid68 2010-04-30T21:41:25Z

The hyperthermostable serine protease pyrolysin from the hyperthermophilic archaeon Pyrococcus furiosus was purified from membrane fractions. Two proteolytically active fractions were obtained, designated high (HMW) and low (LMW) molecular weight pyrolysin, that showed immunological cross-reaction and identical NH2-terminal sequences in which the third residue could be glycosylated. The HMW pyroly...<br/><br/>W G Voorhorst, R I Eggen, A C Geerling, C Platteeuw, R J Siezen, W M Vos (1996) <i>J Biol Chem</i> <i></i> <i></i> 271: 34 20426-20431<br/>

http://publicationslist.org/r.siezen/refid73 2010-04-30T21:41:25Z

R J Siezen (1996) <i>Adv Exp Med Biol</i> <i></i> <i></i> 379: 75-93<br/>

http://publicationslist.org/r.siezen/refid66 2010-04-30T21:41:25Z

Nisin, a 34-residue peptide bacteriocin, contains the less common amino acids lanthionine, beta-methyl-lanthionine, dehydroalanine (Dha), and dehydrobutyrine (Dhb). Several chemically modified nisin A species were purified by reverse-phase HPLC and characterized by two-dimensional NMR and electrospray mass spectrometry. Five constituents, [2-hydroxy-Ala5]nisin, [Ile4-amide,pyruvyl-Leu6]des-Dha5-ni...<br/><br/>H S Rollema, J W Metzger, P Both, O P Kuipers, R J Siezen (1996) <i>Eur J Biochem</i> <i></i> <i></i> 241: 3 716-722<br/>

http://publicationslist.org/r.siezen/refid79 2010-04-30T21:41:25Z

O P Kuipers, H S Rollema, R J Siezen, W M De Vos (1995) <i>Dev Biol Stand</i> <i></i> <i></i> 85: 605-613<br/>

http://publicationslist.org/r.siezen/refid75 2010-04-30T21:41:25Z

Lantibiotics form a family of highly modified peptides which are secreted by several Gram-positive bacteria. They exhibit antimicrobial activity, mainly against other Gram-positive bacteria, by forming pores in the cellular membrane. These antimicrobial peptides are ribosomally synthesized and contain leader peptides which do not show the characteristics of signal sequences. Several amino acid res...<br/><br/>W M de Vos, O P Kuipers, J R van der Meer, R J Siezen (1995) <i>Mol Microbiol</i> <i></i> <i></i> 17: 3 427-437<br/>

http://publicationslist.org/r.siezen/refid77 2010-04-30T21:41:25Z

Lantibiotics are bacteriocins that contain unusual amino acids such as lanthionines and alpha, beta-didehydro residues generated by posttranslational modification of a ribosomally synthesized precursor protein. The structural gene encoding the novel lantibiotic epilancin K7 from Staphylococcus epidermidis K7 was cloned and its nucleotide sequence was determined. The gene, which was named elkA, cod...<br/><br/>M van de Kamp, H W van den Hooven, R N Konings, G Bierbaum, H G Sahl, O P Kuipers, R J Siezen, W M de Vos, C W Hilbers, F J van de Ven (1995) <i>Eur J Biochem</i> <i></i> <i></i> 230: 2 587-600<br/>

http://publicationslist.org/r.siezen/refid78 2010-04-30T21:41:25Z

A model is presented for the 3-D structure of the catalytic domain of the putative leader peptidase NisP of Lactococcus lactis, and the interaction with its specific substrate, the precursor of the lantibiotic nisin. This homology model is based on the crystal structures of subtilisin BPN' and thermitase in complex with the inhibitor eglin. Predictions are made of the general protein fold, inserte...<br/><br/>R J Siezen, H S Rollema, O P Kuipers, W M de Vos (1995) <i>Protein Eng</i> <i></i> <i></i> 8: 2 117-125<br/>

http://publicationslist.org/r.siezen/refid76 2010-04-30T21:41:25Z

Nisin is a 3.4-kDa antimicrobial peptide that, as a result of posttranslational modifications, contains unsaturated amino acids and lanthionine residues. It is applied as a preservative in various food products. The solubility and stability of nisin and nisin mutants have been studied. It is demonstrated that nisin mutants can be produced with improved functional properties. The solubility of nisi...<br/><br/>H S Rollema, O P Kuipers, P Both, W M de Vos, R J Siezen (1995) <i>Appl Environ Microbiol</i> <i></i> <i></i> 61: 8 2873-2878<br/>

http://publicationslist.org/r.siezen/refid83 2010-04-30T21:41:25Z

Structural genes for small lanthionine-containing antimicrobial peptides, known as lantibiotics, encode N-terminal leader sequences which are not present in the mature peptide, but are cleaved off at some stage in the maturation process. Leader sequences of the different lantibiotics share a number of identical amino acid residues, but they are clearly different from sec-dependent protein export s...<br/><br/>J R van der Meer, H S Rollema, R J Siezen, M M Beerthuyzen, O P Kuipers, W M de Vos (1994) <i>J Biol Chem</i> <i></i> <i></i> 269: 5 3555-3562<br/>

http://publicationslist.org/r.siezen/refid82 2010-04-30T21:41:25Z

A model is presented for the three-dimensional structure of the catalytic domain of the human serine proteinase furin and its interaction with model substrates. This homology model is based on the crystal structures of subtilisin BPN' and thermitase in complex with the inhibitor eglin, and it also applies to other members of the eukaryotic subtilisin-like proprotein convertases. Predictions are ma...<br/><br/>R J Siezen, J W Creemers, W J Van de Ven (1994) <i>Eur J Biochem</i> <i></i> <i></i> 222: 2 255-266<br/>

http://publicationslist.org/r.siezen/refid81 2010-04-30T21:41:25Z

The Lactococcus lactis SK11 cell-envelope proteinase contains various inserts, located in external loops of the catalytic domain compared with related subtilisins. In this study, protein engineering was employed to determine the function of the largest loop insertion (residues 238-388) relative to the subtilisin structure. By site-directed mutagenesis we have deleted the fragment of the proteinase...<br/><br/>P G Bruinenberg, P Doesburg, A C Alting, F A Exterkate, W M de Vos, R J Siezen (1994) <i>Protein Eng</i> <i></i> <i></i> 7: 8 991-996<br/>

http://publicationslist.org/r.siezen/refid80 2010-04-30T21:41:25Z

The catalytic domain of the cell-envelope proteinase from Lactococcus lactis SK11 has various inserts, situated in external loops of the catalytic domain, compared with the related subtilisins. Protein engineering was employed to analyse the necessity and function of one of these extra loops (residues 205-219), that is predicted to be located in close proximity to the substrate-binding region and ...<br/><br/>P G Bruinenberg, W M de Vos, R J Siezen (1994) <i>Biochem J</i> <i></i> <i></i> 302 ( Pt 3): 957-963<br/>

http://publicationslist.org/r.siezen/refid87 2010-04-30T21:41:25Z

A cDNA clone containing the entire coding region for bovine beta-casein A3 flanked by 53 base pairs of 5' non-coding and 358 base pairs of 3' non-coding sequences was isolated from a bovine mammary cDNA phagemid library. The coding segment for mature beta-casein was subcloned into the T7 expression system, in which the expression of recombinant beta-casein was controlled by the T7 gene 10 promoter...<br/><br/>G Simons, W van den Heuvel, T Reynen, A Frijters, G Rutten, C J Slangen, M Groenen, W M de Vos, R J Siezen (1993) <i>Protein Eng</i> <i></i> <i></i> 6: 7 763-770<br/>

http://publicationslist.org/r.siezen/refid89 2010-04-30T21:41:25Z

Biosynthesis of the lantibiotic peptide nisin by Lactococcus lactis NIZO R5 relies on the presence of the conjugative transposon Tn5276 in the chromosome. A 12-kb DNA fragment of Tn5276 including the nisA gene and about 10 kb of downstream DNA was cloned in L. lactis, resulting in the production of an extracellular nisin precursor peptide. This peptide reacted with antibodies against either nisin ...<br/><br/>J R van der Meer, J Polman, M M Beerthuyzen, R J Siezen, O P Kuipers, W M De Vos (1993) <i>J Bacteriol</i> <i></i> <i></i> 175: 9 2578-2588<br/>

http://publicationslist.org/r.siezen/refid90 2010-04-30T21:41:25Z

Two natural variants of the lantibiotic nisin that are produced by Lactococcus lactis are known. They have a similar structure but differ in a single amino acid residue at position 27; histidine in nisin A and asparagine in nisin Z (J.W.M. Mulders, I.J. Boerrigter, H.S. Rollema, R.J. Siezen, and W.M. de Vos, Eur. J. Biochem, 201:581-584, 1991). The nisin variants were purified to apparent homogene...<br/><br/>W M de Vos, J W Mulders, R J Siezen, J Hugenholtz, O P Kuipers (1993) <i>Appl Environ Microbiol</i> <i></i> <i></i> 59: 1 213-218<br/>

http://publicationslist.org/r.siezen/refid88 2010-04-30T21:41:25Z

The nisin gene cluster nisABTCIPR of Lactococcus lactis, located on a 10-kbp DNA fragment of the nisin-sucrose transposon Tn5276, was characterized. This fragment was previously shown to direct nisin-A biosynthesis and to contain the nisP and nisR genes, encoding a nisin leader peptidase and a positive regulator, respectively [van der Meer, J. R., Polman, J., Beerthuyzen, M. M., Siezen, R. J., Kui...<br/><br/>O P Kuipers, M M Beerthuyzen, R J Siezen, W M De Vos (1993) <i>Eur J Biochem</i> <i></i> <i></i> 216: 1 281-291<br/>

http://publicationslist.org/r.siezen/refid86 2010-04-30T21:41:25Z

The DNA sequence encoding the leader peptide of the lantibiotic subtilin from Bacillus subtilis was fused to the sequence encoding pronisin Z, and this hybrid gene was expressed in a Lactococcus lactis strain that produces nisin A. This strain simultaneously secreted nisin A and a protein of approximately 6 kDa. Amino acid sequencing of the purified 6 kDa protein and structural analysis of its mai...<br/><br/>O P Kuipers, H S Rollema, W M de Vos, R J Siezen (1993) <i>FEBS Lett</i> <i></i> <i></i> 330: 1 23-27<br/>

http://publicationslist.org/r.siezen/refid85 2010-04-30T21:41:25Z

The proprotein processing activity of mutants of the subtilisin-like enzyme furin was studied in transfected mammalian cells. Our studies indicate that the three residues of the catalytic triad of furin, Asp46, His87, and Ser261, are critical not only for substrate processing but also for maturation of furin. Furthermore, evidence is provided that maturation of furin occurs through an intramolecul...<br/><br/>J W Creemers, R J Siezen, A J Roebroek, T A Ayoubi, D Huylebroeck, W J Van de Ven (1993) <i>J Biol Chem</i> <i></i> <i></i> 268: 29 21826-21834<br/>

http://publicationslist.org/r.siezen/refid84 2010-04-30T21:41:25Z

The substrate-binding region of the cell-envelope proteinase of Lactococcus lactis strain SK11 was modelled, based on sequence homology of the catalytic domain with the serine proteinases subtilisin and thermitase. Substitutions, deletions and insertions were introduced, by site-directed and cassette mutagenesis of the prtP gene encoding this enzyme, based on sequence comparison both with subtilis...<br/><br/>R J Siezen, P G Bruinenberg, P Vos, I van Alen-Boerrigter, M Nijhuis, A C Alting, F A Exterkate, W M de Vos (1993) <i>Protein Eng</i> <i></i> <i></i> 6: 8 927-937<br/>

http://publicationslist.org/r.siezen/refid92 2010-04-30T21:41:25Z

The nucleotide sequence of the pepN gene from Lactococcus lactis encoding a zinc-metallo aminopeptidase has been determined. The open reading frame of 2,538 base pairs encodes a protein with a calculated M(r) of 95,368, which agrees with the apparent M(r) of 95,000 of the gene product which was identified by polyclonal antibodies raised against the purified aminopeptidase. The amino acid sequence ...<br/><br/>P S Tan, I J van Alen-Boerrigter, B Poolman, R J Siezen, W M de Vos, W N Konings (1992) <i>FEBS Lett</i> <i></i> <i></i> 306: 1 9-16<br/>

http://publicationslist.org/r.siezen/refid91 2010-04-30T21:41:25Z

The small antimicrobial peptide nisin, produced by Lactococcus lactis, contains the uncommon amino acid residues dehydroalanine and dehydrobutyrine and five thio ether bridges. Since these structures are posttranslationally formed from Ser, Thr, and Cys residues, it is feasible to study their role in nisin function and biosynthesis by protein engineering. Here we report the development of an expre...<br/><br/>O P Kuipers, H S Rollema, W M Yap, H J Boot, R J Siezen, W M de Vos (1992) <i>J Biol Chem</i> <i></i> <i></i> 267: 34 24340-24346<br/>

http://publicationslist.org/r.siezen/refid95 2010-04-30T21:41:25Z

Plasmids containing wild-type and hybrid proteinase genes were constructed from DNA fragments of the prtP genes of Lactococcus lactis strains Wg2 and SK11. These plasmids were introduced into the plasmid-free strain L. lactis MG1363. The serine proteinases produced by these L. lactis strains were isolated, and their cleavage specificity and rate towards alpha s1- and beta-casein was investigated. ...<br/><br/>P Vos, I J Boerrigter, G Buist, A J Haandrikman, M Nijhuis, M B de Reuver, R J Siezen, G Venema, W M de Vos, J Kok (1991) <i>Protein Eng</i> <i></i> <i></i> 4: 4 479-484<br/>

http://publicationslist.org/r.siezen/refid94 2010-04-30T21:41:25Z

Subtilases are members of the family of subtilisin-like serine proteases. Presently, greater than 50 subtilases are known, greater than 40 of which with their complete amino acid sequences. We have compared these sequences and the available three-dimensional structures (subtilisin BPN', subtilisin Carlsberg, thermitase and proteinase K). The mature enzymes contain up to 1775 residues, with N-termi...<br/><br/>R J Siezen, W M de Vos, J A Leunissen, B W Dijkstra (1991) <i>Protein Eng</i> <i></i> <i></i> 4: 7 719-737<br/>

http://publicationslist.org/r.siezen/refid93 2010-04-30T21:41:25Z

Lactococcus lactis strain NIZO 22186 produces an extracellular, lanthionine-containing 3.5-kDa polypeptide with antimicrobial activity. Its retention time on reversed-phase (RP) HPLC and its amino acid composition showed high similarities but no complete identity to nisin. The gene for this lantibiotic, designated nisZ, has been cloned and its nucleotide sequence was found to be identical to that ...<br/><br/>J W Mulders, I J Boerrigter, H S Rollema, R J Siezen, W M de Vos (1991) <i>Eur J Biochem</i> <i></i> <i></i> 201: 3 581-584<br/>

http://publicationslist.org/r.siezen/refid98 2010-04-30T21:41:25Z

The structural bovine eye lens protein alpha-crystallin was dissociated in 7 M urea and its four subunits, A1, A2, B1, and B2, were separated by means of ion-exchange chromatography. Homopolymeric reaggregates of these subunits were prepared by removal of the denaturant via dialysis. It was found that subunits were exchanged upon incubation of mixtures of two homopolymers under native conditions. ...<br/><br/>P J van den Oetelaar, P F van Someren, J A Thomson, R J Siezen, H J Hoenders (1990) <i>Biochemistry</i> <i></i> <i></i> 29: 14 3488-3493<br/>

http://publicationslist.org/r.siezen/refid96 2010-04-30T21:41:25Z

The human fur gene encodes a protein, designated furin, the C-terminal half of which contains a transmembrane and a cysteine-rich receptor-like domain. The N-terminal half of furin exhibits striking primary amino acid sequence similarity to the catalytic domains of members of the subtilisin family of serine proteases. We here report characteristics of the furin protein and propose a three-dimensio...<br/><br/>W J van de Ven, J Voorberg, R Fontijn, H Pannekoek, A M van den Ouweland, H L van Duijnhoven, A J Roebroek, R J Siezen (1990) <i>Mol Biol Rep</i> <i></i> <i></i> 14: 4 265-275<br/>

http://publicationslist.org/r.siezen/refid97 2010-04-30T21:41:25Z

We have cloned usp45, a gene encoding an extracellular secretory protein of Lactococcus lactis subsp. lactis strain MG1363. Unidentified secreted 45-kDa protein (Usp45) is secreted by every mesophilic L. lactis strain we tested so far and it is chromosomally encoded. The nucleotide sequence of the usp45 gene revealed an open reading frame of 1383 bp encoding a protein of 461 amino acids (aa), comp...<br/><br/>M van Asseldonk, G Rutten, M Oteman, R J Siezen, W M de Vos, G Simons (1990) <i>Gene</i> <i></i> <i></i> 95: 1 155-160<br/>

http://publicationslist.org/r.siezen/refid102 2010-04-30T21:41:25Z

Soluble extracts from young bovine, human, rat and rabbit lenses were fractionated by high resolution size-exclusion chromatography to demonstrate the existence of three discrete size-classes of monomeric crystallins in each species. These were identified by ion exchange chromatography, amino acid analysis, SDS electrophoresis and isoelectric focusing as the beta s-, gamma A- and gamma B-crystalli...<br/><br/>J A Thomson, R J Siezen, E D Kaplan, M Messmer, B Chakrabarti (1989) <i>Curr Eye Res</i> <i></i> <i></i> 8: 2 139-149<br/>

http://publicationslist.org/r.siezen/refid101 2010-04-30T21:41:25Z

Calf lenses which are incubated in solutions of 1-150 mM H2O2 for 24 hr remain clear at 20 degrees C. While insoluble lens protein increases by at most 2-3%, we find extensive oxidation of exposed protein thiols, major shifts in the size distribution of crystallins, and progressive generation of more acidic polypeptides. Some of these oxidative modifications are reversible with reducing agent. bet...<br/><br/>R J Siezen, C M Coppin, E D Kaplan, D Dwyer, J A Thomson (1989) <i>Exp Eye Res</i> <i></i> <i></i> 48: 2 225-235<br/>

http://publicationslist.org/r.siezen/refid100 2010-04-30T21:41:25Z

Measurements were made of lens wet weight, body length and spine diameter of male and female spiny dogfish Squalus acanthias. Age was estimated from body length and spine diameter. It appears that the dogfish eye lens grows continuously during life. Relationships were established between lens weight and age, which allow minimal age to be estimated from lens weight.<br/><br/>R J Siezen (1989) <i>Curr Eye Res</i> <i></i> <i></i> 8: 7 707-712<br/>

http://publicationslist.org/r.siezen/refid99 2010-04-30T21:41:25Z

We have determined the complete nucleotide sequence of the gene for the cell envelope-located proteinase of Lactococcus lactis SK11. The gene contains a very AT-rich promoter region followed by the coding sequence of a protein of 1962 amino acids. Comparison of the NH2-terminal amino acid sequence of the mature proteinase and the expected primary translation product of the proteinase gene indicate...<br/><br/>P Vos, G Simons, R J Siezen, W M de Vos (1989) <i>J Biol Chem</i> <i></i> <i></i> 264: 23 13579-13585<br/>

http://publicationslist.org/r.siezen/refid106 2010-04-30T21:41:25Z

Mammalian lenses contain multiple gamma-crystallin gene products, which are differentially synthesized during lens development. We now report the isolation and characterization of multiple gamma-crystallins from lenses of adult spiny dogfish (Squalus acanthias) aged about 20-30 years. About 50% of total lens protein solubilized in 50 mM phosphate, pH 7.0; about 25% of this soluble fraction consist...<br/><br/>R J Siezen, C Hom, E D Kaplan, J A Thomson, G B Benedek (1988) <i>Exp Eye Res</i> <i></i> <i></i> 46: 1 81-93<br/>

http://publicationslist.org/r.siezen/refid105 2010-04-30T21:41:25Z

We have isolated, purified and characterized six individual gamma-crystallin polypeptides present in the rat lens. Comparison of their amino acid compositions with the known structure of the six gamma-crystallin genes permits a one-to-one correspondence to be made between each protein synthesized and the encoding gene. This demonstrates that each of the six genes is actually expressed in vivo. Two...<br/><br/>R J Siezen, E Wu, E D Kaplan, J A Thomson, G B Benedek (1988) <i>J Mol Biol</i> <i></i> <i></i> 199: 3 475-490<br/>

http://publicationslist.org/r.siezen/refid104 2010-04-30T21:41:25Z

R J Siezen (1988) <i>Exp Eye Res</i> <i></i> <i></i> 46: 6 987-990<br/>

http://publicationslist.org/r.siezen/refid103 2010-04-30T21:41:25Z

Cation-exchange high-performance liquid chromatography on SynChropak CM300 in Tris-acetate buffers of pH 5-7, using sodium acetate gradients, produces an excellent separation of the various gamma-crystallin gene products and their post-synthetically modified forms from eye lens. With a single analysis of total lens extract, the gamma-crystallins can be resolved, quantified and collected for amino ...<br/><br/>R J Siezen, E D Kaplan (1988) <i>J Chromatogr</i> <i></i> <i></i> 444: 239-250<br/>

http://publicationslist.org/r.siezen/refid108 2010-04-30T21:41:25Z

The denaturation behavior of bovine lens gamma-crystallin fractions II, III, and IV and their susceptibility to proteolysis in vitro was compared to determine whether differences in their stability could play a role in cataract formation. Tertiary and secondary structure changes induced by increasing concentrations of urea, guanidine hydrochloride, and sodium dodecyl sulfate and by increasingly al...<br/><br/>K Mandal, B Chakrabarti, J Thomson, R J Siezen (1987) <i>J Biol Chem</i> <i></i> <i></i> 262: 17 8096-8102<br/>

http://publicationslist.org/r.siezen/refid109 2010-04-30T21:41:25Z

The gamma-crystallin fractions II, III and IV from calf eye lens were treated with the thiol-specific fluorescent probe 2-(4'-maleimidylanilino)naphthalene-6-sulfonate (MIANS), in order to determine the reactivity of the seven (gamma-II) or six (gamma-III, gamma-IV) cysteine residues. Two classes of reactive cysteines were distinguished by variations in fluorescence intensity with increasing molar...<br/><br/>K Mandal, S K Bose, B Chakrabarti, R J Siezen (1987) <i>Biochim Biophys Acta</i> <i></i> <i></i> 911: 3 277-284<br/>

http://publicationslist.org/r.siezen/refid107 2010-04-30T21:41:25Z

We have isolated the individual gamma-crystallins expressed in young human lenses and identified with which of the six known human gamma-crystallin genes they each correspond. We find that at least 90% of the gamma-crystallins synthesized in the young human lens are the products of genes gamma G3 and gamma G4. We demonstrate that gamma G4-crystallin undergoes a temperature-dependent phase separati...<br/><br/>R J Siezen, J A Thomson, E D Kaplan, G B Benedek (1987) <i>Proc Natl Acad Sci U S A</i> <i></i> <i></i> 84: 17 6088-6092<br/>

http://publicationslist.org/r.siezen/refid110 2010-04-30T21:41:25Z

The concentration-dependence of beta-crystallin aggregation was studied by both high- and low-pressure size exclusion chromatography of calf lens cortical extract (0.5-249 mg ml-1), nuclear extract (0.2-304 mg ml-1) and purified beta-crystallins (0.4-52 mg ml-1). A reversible equilibrium exists between beta H(igh)-crystallins (predominantly hexamers) and a portion of the beta L(ow)-crystallins (pr...<br/><br/>R J Siezen, R D Anello, J A Thomson (1986) <i>Exp Eye Res</i> <i></i> <i></i> 43: 3 293-303<br/>

http://publicationslist.org/r.siezen/refid115 2010-04-30T21:41:25Z

A novel procedure is presented for the rapid quantitative analysis of eye lens gamma-crystallins and beta s-crystallin by ion-exchange high-performance liquid chromatography on Synchropak CM300. At least six different gamma-crystallin gene products can be resolved from the soluble fraction of calf lens extract. This method is applicable to the analysis of microsections from individual lenses, and ...<br/><br/>R J Siezen, E D Kaplan, R D Anello (1985) <i>Biochem Biophys Res Commun</i> <i></i> <i></i> 127: 1 153-160<br/>

http://publicationslist.org/r.siezen/refid114 2010-04-30T21:41:25Z

To determine the molecular mechanisms for cold cataract formation in the nucleus of the young mammalian lens, we have investigated the thermally reversible opacification of gamma-crystallin solutions isolated from calf lens. Coexistence curves (plots of opacification temperature Tc versus protein concentration) were determined for the individual gamma-crystallin fractions II, III, and IV as well a...<br/><br/>R J Siezen, M R Fisch, C Slingsby, G B Benedek (1985) <i>Proc Natl Acad Sci U S A</i> <i></i> <i></i> 82: 6 1701-1705<br/>

http://publicationslist.org/r.siezen/refid112 2010-04-30T21:41:25Z

Low temperature induced opacification (cold cataract) of the nucleus of young mammalian lenses is associated with a phase separation of proteins in the lens cell cytoplasm. Calf lenses were treated with a variety of imido-esters and N-hydroxysuccinimide-esters, which react specifically with amino groups. Many potent inhibitors of phase separation cataract were identified which lower the opacificat...<br/><br/>R J Siezen, C M Coppin, G B Benedek (1985) <i>Biochem Biophys Res Commun</i> <i></i> <i></i> 133: 1 239-247<br/>

http://publicationslist.org/r.siezen/refid113 2010-04-30T21:41:25Z

In the bovine lens the gamma IV-crystallin fraction is a principal determinant of the phase separation and opacification temperature, Tc (Siezen et al, Proc. Natl. Acad. Sci. USA 82, 1985, 1701). We have now measured the effect on Tc of purified gamma IV-crystallin solutions produced by a variety of reagents which affect protein-protein, protein-water and water-water interactions. Ionic strengths ...<br/><br/>R J Siezen, G B Benedek (1985) <i>Curr Eye Res</i> <i></i> <i></i> 4: 10 1077-1085<br/>

http://publicationslist.org/r.siezen/refid111 2010-04-30T21:41:25Z

The three major bovine gamma-crystallin fractions (gamma-II, gamma-III and gamma-IV) are known to have closely related (80-90%) amino acid sequences and three-dimensional folding of the polypeptide backbone. Their chiroptical and emission properties, as measured by circular dichroism (CD) and fluorescence, are now shown to differ distinctly. The far-ultraviolet CD spectra indicate that all three g...<br/><br/>K Mandal, S K Bose, B Chakrabarti, R J Siezen (1985) <i>Biochim Biophys Acta</i> <i></i> <i></i> 832: 2 156-164<br/>

http://publicationslist.org/r.siezen/refid118 2010-04-30T21:41:25Z

Crystallins from calf lens were subjected to ultrafiltration through an Amicon XM-300 membrane to determine whether specific interactions between identical proteins (self-association) or different proteins (mixed-association) could be detected and quantified. Single crystallins at different concentrations, simple mixtures and total lens extracts were studied separately. alpha-Crystallin (Mr 800 00...<br/><br/>R J Siezen (1984) <i>Biophys Chem</i> <i></i> <i></i> 19: 1 49-55<br/>

http://publicationslist.org/r.siezen/refid116 2010-04-30T21:41:25Z

The 'microheterogeneity model' (R.J. Siezen and R. van Driel, Biochim. Biophys. Acta 295 (1973) 131) and the 'incompetent whole molecule model' (G. Kegeles, Arch. Biochem. Biophys. 180 (1977) 530) for the dissociation of Helix pomatia alpha-hemocyanin whole molecules to half molecules were tested experimentally, using ultracentrifugation and stopped-flow dilution analysis. Results of differential ...<br/><br/>R J Siezen, E F van Bruggen, M S Tai, M C Crossin, G Kegeles (1984) <i>Biophys Chem</i> <i></i> <i></i> 19: 2 99-112<br/>

http://publicationslist.org/r.siezen/refid117 2010-04-30T21:41:25Z

R J Siezen (1984) <i>Exp Eye Res</i> <i></i> <i></i> 38: 2 207-210<br/>

http://publicationslist.org/r.siezen/refid123 2010-04-30T21:41:25Z

A competitive radioimmunoassay was used to determine the reactivities of alpha-crystallins from 13 species with antibodies directed toward calf alpha-crystallin. The results indicate that species as diverse as human and dogfish share the same number of crossreacting antigenic determinants. The various alpha-crystallins can be distinguished only on the basis of their differing affinities for the an...<br/><br/>N Puri, R C Augusteyn, E A Owen, R J Siezen (1983) <i>Eur J Biochem</i> <i></i> <i></i> 134: 2 321-326<br/>

http://publicationslist.org/r.siezen/refid122 2010-04-30T21:41:25Z

Concentrated solutions of calf alpha-crystallin (up to 45 g/l) and gamma-crystallin (up to 67 g/l) were subjected to frontal exclusion chromatography at pH 7.3, ionic strength 0.17 and 20 degrees C. The experimental concentration dependence of the weight-average partition coefficient was compared with theoretical expressions, which include considerations of thermodynamic non-ideality effects, for ...<br/><br/>R J Siezen, E A Owen (1983) <i>Biophys Chem</i> <i></i> <i></i> 18: 3 181-194<br/>

http://publicationslist.org/r.siezen/refid124 2010-04-30T21:41:25Z

The X-ray crystallographic structure of bovine gamma-crystallin shows four similar folding motifs each composed of about 42 residues arranged as four topologically sequential, anti-parallel beta-strands. Since the beta and gamma-crystallin sequences show good homology, proposals for a four-motif beta-crystallin model have been made. The other bovine eye-lens protein species, alpha-crystallins, are...<br/><br/>P Argos, R J Siezen (1983) <i>Eur J Biochem</i> <i></i> <i></i> 131: 1 143-148<br/>

http://publicationslist.org/r.siezen/refid119 2010-04-30T21:41:25Z

Calf lens nuclear alpha-crystallin was separated into five molecular weight subpopulations by exclusion chromatography on Bio-Gel A-5m. These subpopulations were compared by amino acid analysis, ultraviolet absorption analysis, fluorescence, far- and near-ultraviolet circular dichroism, isoelectric focusing, SDS-polyacrylamide gel electrophoresis and sedimentation velocity analysis. Although only ...<br/><br/>R J Siezen, E A Owen (1983) <i>Biochim Biophys Acta</i> <i></i> <i></i> 749: 3 227-237<br/>

http://publicationslist.org/r.siezen/refid120 2010-04-30T21:41:25Z

Circular dichroism spectra (196-240 nm) of calf alpha-, beta H-, beta L- and gamma-crystallins were measured and analyzed over the entire wavelength range with five curve-fitting procedures for estimating protein secondary structure. For gamma-crystallin the estimates are in good agreement with the X-ray structure. For all four crystallins the estimates are very similar: 0-9% alpha-helix and 51-68...<br/><br/>R J Siezen, P Argos (1983) <i>Biochim Biophys Acta</i> <i></i> <i></i> 748: 1 56-67<br/>

http://publicationslist.org/r.siezen/refid121 2010-04-30T21:41:25Z

Bovine lens alpha A- and alpha B-crystallin polypeptides show extensive sequence homology with each other, but apparently none with beta Bp- and gamma 2-crystallin. Despite only 30% sequence homology, the latter two proteins are assumed to have a strong correspondence in tertiary structure, consisting of four structurally similar folding units of antiparallel beta-sheet. We have tested for interna...<br/><br/>R J Siezen, E A Owen, Y Kubota, T Ooi (1983) <i>Biochim Biophys Acta</i> <i></i> <i></i> 748: 1 48-55<br/>

http://publicationslist.org/r.siezen/refid127 2010-04-30T21:41:25Z

Cytoskeletal and membrane proteins were isolated from respectively the urea-soluble and urea-insoluble fractions of the squid lens. The main cytoskeletal polypeptide has a molecular weight (63000) and an amino acid composition similar to those of vertebrate intermediate filament proteins, including mammalian lens vimentins. Intermediate filaments, and bundles thereof, were regenerated from the squ...<br/><br/>R J Siezen (1982) <i>Curr Eye Res</i> <i></i> <i></i> 2: 9 579-589<br/>

http://publicationslist.org/r.siezen/refid126 2010-04-30T21:41:25Z

R J Siezen, J G Bindels (1982) <i>Exp Eye Res</i> <i></i> <i></i> 34: 6 969-983<br/>

http://publicationslist.org/r.siezen/refid125 2010-04-30T21:41:25Z

The main water-soluble proteins of squid lens (S-crystallins) have a molecular weight of 60 000, a sedimentation coefficient s020,w of 5.2 S, 20-30% alpha-helical secondary structure, and an unusually high methionine content (12%). The subunits of Mr 30 000 (major) and Mr 27 000 (minor) have related N-terminal amino acid sequences, but a very heterogeneous charge distribution with predominantly ba...<br/><br/>R J Siezen, D C Shaw (1982) <i>Biochim Biophys Acta</i> <i></i> <i></i> 704: 2 304-320<br/>

http://publicationslist.org/r.siezen/refid129 2010-04-30T21:41:25Z

R J Siezen (1981) <i>FEBS Lett</i> <i></i> <i></i> 133: 1 1-8<br/>

http://publicationslist.org/r.siezen/refid128 2010-04-30T21:41:25Z

Theory pertaining to the interpretation of partition chromatography results obtained with self-associating protein systems studied at high total concentrations is extended to permit consideration of situations in which both monomeric and dimeric states partition. This development, which includes considerations of thermodynamic nonideality effects, permits a quantitative correlation of human oxyhem...<br/><br/>R J Siezen, L W Nichol, D J Winzor (1981) <i>Biophys Chem</i> <i></i> <i></i> 14: 3 221-231<br/>

http://publicationslist.org/r.siezen/refid131 2010-04-30T21:41:25Z

An improved iterative method for computing association constants from sedimentation equilibrium results obtained with self-interacting protein systems is presented which accounts for the composition-dependence of the activity coefficients of all oligomeric species. The method is based on the calculation of viral coefficients from covolume and charge considerations, the statistical mechanical basis...<br/><br/>P R Wills, L W Nichol, R J Siezen (1980) <i>Biophys Chem</i> <i></i> <i></i> 11: 1 71-82<br/>

http://publicationslist.org/r.siezen/refid132 2010-04-30T21:41:25Z

Reaction of calf alpha-crystallin, which consists of about 30 A and 10 B subunits, with various bisimido esters at pH 8.0-8.5 and room temperature leads to inter-subunit crosslinking. Little difference is observed in the efficiency of crosslinking by reagents of a homologous series with different lengths (from C6 to C12). At any stage of the reaction an exponential decrease is found in the amounts...<br/><br/>R J Siezen, J G Bindels, H J Hoenders (1980) <i>Eur J Biochem</i> <i></i> <i></i> 107: 1 243-249<br/>

http://publicationslist.org/r.siezen/refid130 2010-04-30T21:41:25Z

The stability of the native quaternary structure of bovine alpha-crystallin was studied, by sedimentation analysis and electron microscopy, as a function of pH (7--11), ionic strength (0.01--0.5), temperature (6--60 degrees C) and calcium ion concentration (0 and 10 mM). Three successive transitions are distinguished at 20 degrees C. Firstly, a slow transconformation step, which is independent of ...<br/><br/>R J Siezen, J G Bindels, H J Hoenders (1980) <i>Eur J Biochem</i> <i></i> <i></i> 111: 2 435-444<br/>

http://publicationslist.org/r.siezen/refid136 2010-04-30T21:41:25Z

R J Siezen (1979) <i>FEBS Lett</i> <i></i> <i></i> 100: 1 75-80<br/>

http://publicationslist.org/r.siezen/refid135 2010-04-30T21:41:25Z

R J Siezen, J G Bindels, H J Hoenders (1979) <i>Exp Eye Res</i> <i></i> <i></i> 28: 5 551-567<br/>

http://publicationslist.org/r.siezen/refid134 2010-04-30T21:41:25Z

R J Siezen, H J Hoenders (1979) <i>Eur J Biochem</i> <i></i> <i></i> 96: 3 431-440<br/>

http://publicationslist.org/r.siezen/refid133 2010-04-30T21:41:25Z

Expressions that take into account the effects of thermodynamic non-ideality, described in terms of a high-order virial expansion, are derived for the concentration-dependence of the weight-average partition coefficient in exclusion chromatography of a single solute and of a solute undergoing reversible self-association. Comparison of the concentration-dependences predicted by those expressions wi...<br/><br/>L W Nichol, R J Siezen, D J Winzor (1979) <i>Biophys Chem</i> <i></i> <i></i> 10: 1 17-26<br/>

http://publicationslist.org/r.siezen/refid140 2010-04-30T21:41:25Z

L W Nichol, R J Siezen, D J Winzor (1978) <i>Biophys Chem</i> <i></i> <i></i> 9: 1 47-55<br/>

http://publicationslist.org/r.siezen/refid139 2010-04-30T21:41:25Z

R J Siezen, H Berger (1978) <i>Eur J Biochem</i> <i></i> <i></i> 91: 2 397-405<br/>

http://publicationslist.org/r.siezen/refid138 2010-04-30T21:41:25Z

Cortial alpha-crystallin was size-fractionated by gel filtration on Ultrogel AcA22 and charge-fractionated by anion-exchange chromatography on DE-52 DEAE-cellulose using gradient elution. Electron microscopy demonstrates that both native and reassociated alpha-crystallin are heterogeneous populations of spherical or slightly ellipsoidal molecules with diameters of 13.5--16.0 nm (maximum at 14.0--1...<br/><br/>R J Siezen, J G Bindels, H J Hoenders (1978) <i>Eur J Biochem</i> <i></i> <i></i> 91: 2 387-396<br/>

http://publicationslist.org/r.siezen/refid137 2010-04-30T21:41:25Z

alpha-Crystallin from calf eye lens is found to have 30 sulfhydryl groups per 800 000 daltons by modification with 5,5'-dithiobis-(2-nitrobenzoic acid) (DTNB) and 4,4'-dithiopyridine in 6 M urea. These -SH groups can be divided into three different classes in native alpha-crystallin from their reactivity with DTNB, 4,4'-dithiopyridine, iodoacetamide and ethylenimine. Results obtained with these re...<br/><br/>R J Siezen, F G Coenders, H J Hoenders (1978) <i>Biochim Biophys Acta</i> <i></i> <i></i> 537: 2 456-465<br/>

http://publicationslist.org/r.siezen/refid142 2010-04-30T21:41:25Z

Fifty amino acids are analyzed as their N-heptafluorobutyryl isobutyl esters by gas chromatography on a column of 3% OV-101 on Gas-Chrom Q. The identification and quantification of unusual amino acids, specifically those occurring in the marine environment, in the presence of common protein amino acids is reported. Regular relationships between elution temperatures and amino acid structures are fo...<br/><br/>R J Siezen, T H Mague (1977) <i>J Chromatogr</i> <i></i> <i></i> 130: 151-160<br/>

http://publicationslist.org/r.siezen/refid141 2010-04-30T21:41:25Z

R J Siezen, H J Hoenders (1977) <i>FEBS Lett</i> <i></i> <i></i> 80: 1 75-80<br/>

http://publicationslist.org/r.siezen/refid145 2010-04-30T21:41:25Z

R J Siezen (1974) <i>J Mol Biol</i> <i></i> <i></i> 90: 1 103-113<br/>

http://publicationslist.org/r.siezen/refid143 2010-04-30T21:41:25Z

R J Siezen, R van Driel (1974) <i>J Mol Biol</i> <i></i> <i></i> 90: 1 91-102<br/>

http://publicationslist.org/r.siezen/refid144 2010-04-30T21:41:25Z

R J Siezen, E F van Bruggen (1974) <i>J Mol Biol</i> <i></i> <i></i> 90: 1 77-89<br/>

http://publicationslist.org/r.siezen/refid146 2010-04-30T21:41:25Z

R J Siezen, R van Driel (1973) <i>Biochim Biophys Acta</i> <i></i> <i></i> 295: 1 131-139<br/>

http://publicationslist.org/r.siezen/refid147 2010-04-30T21:41:25Z

W N Konings, R J Siezen, M Gruber (1969) <i>Biochim Biophys Acta</i> <i></i> <i></i> 194: 2 376-385<br/>