A portal for rhizobial genomes: RhizoGATE integrates a Sinorhizobium meliloti genome annotation update with postgenome data

Abstract

Sinorhizobium meliloti is a symbiotic soil bacterium of the alphaproteobacterial subdivision. Like other rhizobia, S. meliloti induces nitrogen-fixing root nodules on leguminous plants. This is an ecologically and economically important interaction, because plants engaged in symbiosis with rhizobia can grow without exogenous nitrogen fertilizers. The S. meliloti-Medicago truncatula (barrel medic) association is an important symbiosis model. The S. meliloti genome was published in 2001, and the Medicago truncatula genome currently is being sequenced. Many new resources and data have been made available since the original S. meliloti genome annotation and an update was needed. In June 2008, we submitted our annotation update to the EMBL and NCBI databases. Here we describe this new annotation and a new web-based portal RhizoGATE. About 1000 annotation updates were made; these included assigning functions to 313 putative proteins, assigning EC numbers to 431 proteins, and identifying 86 new putative genes. RhizoGATE incorporates the new annotion with the S. meliloti GenDB project, a platform that allows annotation updates in real time. Locations of transposon insertions, plasmid integrations, and array probe sequences are available in the GenDB project. RhizoGATE employs the EMMA platform for management and analysis of transcriptome data and the IGetDB data warehouse to integrate a variety of heterogeneous external data sources.

An ABC-Type Cobalt Transport System Is Essential for Growth of Sinorhizobium melilotiat Trace Metal Concentrations

“…These encode a periplasmic substrate-binding protein (CbtJ), a permease (CbtK), and an ATP-binding protein (CbtL) of an ABC-type transport system. As discussed below, these genes were reannotated btuF, btuC, and btuD in the current S. meliloti genome database (4). Based on our data and unpublished work (J. Cheng et al, submitted for publication), we have designated these genes the cobalt transporter genes cbtJ, cbtK, and cbtL, respectively, and we use these names throughout this work.…”

“…In previous reports based on informatics, the smb20056, smb20057, and smb20058 genes were designated btuFCD genes encoding a vitamin B 12 transport system (4,69). In another report, on the basis of mRNA transcript nucleotide sequencing, Mao et al (39) suggested that a small, 180-nucleotide open reading frame (vbismb0078) is located in the 5Ј-UTR of cbtJ.…”

“…Co 2ϩ is required for the growth of S. meliloti and other rhizobia (36,70) and is required for efficient nitrogen fixation in the Sinorhizobium-alfalfa symbiosis (15). S. meliloti synthesizes vitamin B 12 , and the Cbl-dependent enzymes methylmalonyl-coenzyme A (CoA) mutase, methionine synthase, and ribonucleotide reductase have been identified (9,10,14,30,62), as well as putative Cbl biosynthetic genes (4). The S. meliloti BluB protein was recently shown to catalyze a missing step in vitamin B 12 synthesis by cannibalizing flavin to form 5,6-dimethylbenzimidazole, the lower ligand of vitamin B 12 (7,67).…”

AraC-like transcriptional activator CuxR binds c-di-GMP by a PilZ-like mechanism to regulate extracellular polysaccharide production

“…To determine whether increased transcription of this operon was responsible for enhanced CR staining, we interrupted the putative uxs1-SMb20463 operon by integration of pK19mob2ΩHMB-uxe (40) into uxe in wild-type S. meliloti and in the mucR mutant. Integration of pK19mob2ΩHMB has been shown to disrupt transcription due to a strong transcription terminator encoded by this plasmid (40).…”

Genome-wide profiling of Hfq-binding RNAs uncovers extensive post-transcriptional rewiring of major stress response and symbiotic regulons inSinorhizobium meliloti

“…79 Next to 6296 protein-coding genes, the annotation of S. meliloti 1021 includes 545 trans-sRNAs, 3028 asRNAs, and the positions of TSS defining the 5′-UTR of 2832 mRNAs, all discovered in previous studies. 23,39 Sequencing reads from the five Hfq and the two control (C) CoIP cDNA libraries were preprocessed and individually mapped to the S. meliloti 1021 genome using Segemehl with standard parameters.…”