Conversion of Methionine to Cysteine in Lactobacillus paracasei Depends on the Highly Mobile cysK-ctl-cysE Gene Cluster

Milk and dairy products are rich in nutrients and are therefore habitats for various microbiomes. However, the composition of nutrients can be quite diverse, in particular among the sulfur containing amino acids. In milk, methionine is present in a 25-fold higher abundance than cysteine. Interestingly, a fraction of strains of the species L. paracasei – a flavor-enhancing adjunct culture species – can grow in medium with methionine as the sole sulfur source. In this study, we focus on genomic and evolutionary aspects of sulfur dependence in L. paracasei strains. From 24 selected L. paracasei strains, 16 strains can grow in medium with methionine as sole sulfur source. We sequenced these strains to perform gene-trait matching. We found that one gene cluster – consisting of a cysteine synthase, a cystathionine lyase, and a serine acetyltransferase – is present in all strains that grow in medium with methionine as sole sulfur source. In contrast, strains that depend on other sulfur sources do not have this gene cluster. We expanded the study and searched for this gene cluster in other species and detected it in the genomes of many bacteria species used in the food production. The comparison to these species showed that two different versions of the gene cluster exist in L. paracasei which were likely gained in two distinct events of horizontal gene transfer. Additionally, the comparison of 62 L. paracasei genomes and the two versions of the gene cluster revealed that this gene cluster is mobile within the species.

[1]  R. Bruggmann,et al.  Transcriptional Regulation of Cysteine and Methionine Metabolism in Lactobacillus paracasei FAM18149 , 2018, Front. Microbiol..

[2]  Richard A Neher,et al.  panX: pan-genome analysis and exploration , 2016, bioRxiv.

[3]  F. Biasioli,et al.  Phylogenomic Analysis of Oenococcus oeni Reveals Specific Domestication of Strains to Cider and Wines , 2015, Genome biology and evolution.

[4]  Andrew J. Page,et al.  Roary: rapid large-scale prokaryote pan genome analysis , 2015, bioRxiv.

[5]  W. Hanage,et al.  Global Phylogenomic Analysis of Nonencapsulated Streptococcus pneumoniae Reveals a Deep-Branching Classic Lineage That Is Distinct from Multiple Sporadic Lineages , 2014, Genome biology and evolution.

[6]  Torsten Seemann,et al.  Prokka: rapid prokaryotic genome annotation , 2014, Bioinform..

[7]  Katharina Breme,et al.  A preliminary study on the effect of Lactobacillus casei expressing cystathionine lyase1/cystathionine lyase2 on Cheddar cheese and the formation of sulphur-containing compounds , 2013 .

[8]  R. Siezen,et al.  Lactobacillus paracasei Comparative Genomics: Towards Species Pan-Genome Definition and Exploitation of Diversity , 2013, PloS one.

[9]  Aaron A. Klammer,et al.  Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data , 2013, Nature Methods.

[10]  Richard P. Evershed,et al.  Earliest evidence for cheese making in the sixth millennium bc in northern Europe , 2012, Nature.

[11]  N. Perna,et al.  Analysis of the Lactobacillus casei supragenome and its influence in species evolution and lifestyle adaptation , 2012, BMC Genomics.

[12]  W. Pirovano,et al.  Toward almost closed genomes with GapFiller , 2012, Genome Biology.

[13]  Hamidreza Chitsaz,et al.  SEQuel: improving the accuracy of genome assemblies , 2012, Bioinform..

[14]  Paul D. Cotter,et al.  High-Throughput Sequencing for Detection of Subpopulations of Bacteria Not Previously Associated with Artisanal Cheeses , 2012, Applied and Environmental Microbiology.

[15]  R. Portmann,et al.  CysK from Lactobacillus casei encodes a protein with O-acetylserine sulfhydrylase and cysteine desulfurization activity , 2012, Applied Microbiology and Biotechnology.

[16]  Sergey I. Nikolenko,et al.  SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing , 2012, J. Comput. Biol..

[17]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[18]  R. Portmann,et al.  Characterization of the cysK2-ctl1-cysE2 gene cluster involved in sulfur metabolism in Lactobacillus casei. , 2012, International journal of food microbiology.

[19]  D. Higgins,et al.  Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega , 2011, Molecular systems biology.

[20]  W. Pirovano,et al.  Scaffolding pre-assembled contigs using SSPACE , 2011, Bioinform..

[21]  Kung-Sik Chan,et al.  Introducing COZIGAM: An R Package for Unconstrained and Constrained Zero-Inflated Generalized Additive Model Analysis , 2010 .

[22]  N. Perna,et al.  progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement , 2010, PloS one.

[23]  Miriam L. Land,et al.  Trace: Tennessee Research and Creative Exchange Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification Recommended Citation Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification , 2022 .

[24]  Hadley Wickham,et al.  ggplot2 - Elegant Graphics for Data Analysis (2nd Edition) , 2017 .

[25]  J. Steele,et al.  Genome Sequence and Comparative Genome Analysis of Lactobacillus casei: Insights into Their Niche-Associated Evolution , 2009, Genome biology and evolution.

[26]  H. Berthoud,et al.  Identification and characterization of a strain-dependent cystathionine beta/gamma-lyase in Lactobacillus casei potentially involved in cysteine biosynthesis. , 2009, FEMS microbiology letters.

[27]  R. Siezen,et al.  In Silico Prediction of Horizontal Gene Transfer Events in Lactobacillus bulgaricus and Streptococcus thermophilus Reveals Protocooperation in Yogurt Manufacturing , 2009, Applied and Environmental Microbiology.

[28]  Fiona S. L. Brinkman,et al.  IslandViewer: an integrated interface for computational identification and visualization of genomic islands , 2009, Bioinform..

[29]  C. Francke,et al.  Comparative Genomics of Enzymes in Flavor-Forming Pathways from Amino Acids in Lactic Acid Bacteria , 2008, Applied and Environmental Microbiology.

[30]  Katherine H. Huang,et al.  Comparative genomics of the lactic acid bacteria , 2006, Proceedings of the National Academy of Sciences.

[31]  Alexandros Stamatakis,et al.  RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models , 2006, Bioinform..

[32]  C. Stoeckert,et al.  OrthoMCL: identification of ortholog groups for eukaryotic genomes. , 2003, Genome research.

[33]  J. Steele,et al.  Impaired Growth Rates in Milk of Lactobacillus helveticus Peptidase Mutants Can Be Overcome by Use of Amino Acid Supplements , 2003, Journal of bacteriology.

[34]  W. P. Hammes,et al.  The genera Lactobacillus and Carnobacterium , 1992 .

[35]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[36]  M. Collins,et al.  Deoxyribonucleic Acid Homology Studies of Lactobacillus casei, Lactobacillus paracasei sp. nov., subsp. paracasei and subsp. tolerans, and Lactobacillus rhamnosus sp. nov., comb. nov. , 1989 .

[37]  L. G. Wayne.  Actions of the Judicial Commission of the International Committee on Systematic Bacteriology on Requests for Opinions Published in 1983 and 1984 , 1986 .

[38]  L. G. Wayne.  Actions of the Judicial Commission of the International Committee on Systematic Bacteriology on Requests for Opinions Published Between January 1985 and July 1993 , 1982 .

[39]  M. Rogosa,et al.  A MEDIUM FOR THE CULTIVATION OF LACTOBACILLI , 1960 .

[40]  T. Lumley,et al.  gplots: Various R Programming Tools for Plotting Data , 2015 .

[41]  I. Piedade,et al.  In silico prediction of , 2014 .

[42]  Cedric E. Ginestet.  ggplot2: Elegant Graphics for Data Analysis , 2011 .

[43]  R. Fisher.  On the Interpretation of χ2 from Contingency Tables, and the Calculation of P , 2010 .

[44]  F. Delsuc.  Comparative Genomics , 2010, Lecture Notes in Computer Science.

[45]  Peer Bork,et al.  Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation , 2007, Bioinform..

[46]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[47]  R. Fisher.  019: On the Interpretation of x2 from Contingency Tables, and the Calculation of P. , 1922 .