The genome organization of porcine respiratory coronavirus (PRCV), a newly recognized agent which has a close antigenic relationship to the enteropathogenic transmissible gastroenteritis virus (TGEV), was studied. Genomic RNA from cell-cultured PRCV (French isolate RM4) was used to produce eDNA clones covering the genomic 3' end to the start of the spike (S) glycoprotein gene (7519 nucleotides). Six open reading frames (ORFs) were identified that allowed the translation of three coronavirus structural proteins and three putative non-structural (NS) polypeptides, homologous to TGEV ORFs designated NS3-1, NS4 and NS7. Pairwise alignment of PRCV nucleotide and amino acid sequences with sequence data available for three TGEV strains revealed a 96 % overall homology. However, the genome of PRCV exhibited two important distinctive features. The first was that the S gene lacked 672 nucleotides in the 5' region and encoded a truncated form of the S polypeptide, and secondly, the first NS ORF downstream of the S gene was predicted to be non-functional as a consequence of a double deletion. The significance ofgenomic deletions with respect to tissue tropism and evolution of coronaviruses is discussed.

In order to investigate the genome organization of the porcine epidemic diarrhea virus (PEDV) further, cDNA clones covering the region between the nucleocapsid and the spike (S) protein genes were independently constructed and sequenced for the two virulent isolates Br1/87 and CV777. Of the three major ORFs identified, two were found to encode the major and minor coronavirus membrane proteins M and sM. A potentially single ORF, designated ORF3 according to the pattern of the viral subgenomic mRNAs, could be identified between the S and sM genes. A striking variability, essentially generated by short deletions clustered in a few loci, was observed in the ORF3 of both isolates. The largest predicted polypeptide of 223 amino acids showed homology with polypeptides potentially encoded by other members of the same genetic subset, including two shorter polypeptides of human respiratory virus HCV 229E and one of transmissible gastroenteritis virus TGEV. This homology suggests that the two HCV ORFs may have originated from a single precursor. The function of these polypeptides is not known, but the predicted products of the PEDV ORF3 and related ORFs share features suggestive of a membrane-associated protein.

The complete sequence of the spike (S) gene of the Brl/87 isolate of porcine epidemic diarrhoea virus (PEDV) was determined from cDNA clones. The predicted polypeptide was 1383 amino acids long, contained 29 potential N-linked glycosylation sites and showed structural features similar to those of the coronavirus spike protein. The PEDV S protein, like that of the members of the transmissible gastroenteritis virus (TGEV)-related subset, lacks a proteolytic site to yield cleaved amino and carboxy subunits S1 and $2. Viral polypeptide species of the expected Mr, i.e. 170K/190K, were observed in PEDV-infected cells. Sequence comparison confirmed that, within the subset, PEDV was most closely related to the human respiratory coronavirus HCV 229E. However, PEDV S protein has an additional 250 residue N-terminal domain which is absent from HCV 229E and porcine respiratory coronavirus, the respiratory variant of TGEV. Alignment of the S1 regions revealed a second domain of about 90 residues with increased sequence divergence which might possibly express virus-specific determinants.

Rotavirus NSP5 is a non-structural phosphoprotein with putative autocatalytic kinase activity, and is present in infected cells as various isoforms having molecular masses of 26, 28 and 30-34 kDa. We have previously shown that NSP5 forms oligomers and interacts with NSP6 in yeast cells. Here we have mapped the domains of NSP5 responsible for these associations. Deletion mutants of the rotavirus YM NSP5 were constructed and assayed for their ability to interact with full-length NSP5 and NSP6 using the yeast two-hybrid assay. The homomultimerization domain was mapped to the 20 C-terminal aa of the protein, which have a predicted α-helical structure. A deletion mutant lacking the 10 C-terminal aa (∆C10) failed to multimerize both in yeast cells and in an in vitro affinity assay. When transiently expressed in MA104 cells, NSP5 became hyperphosphorylated (30-34 kDa isoforms). In contrast, the ∆C10 mutant produced forms equivalent to the 26 and 28 kDa species, but was poorly hyperphosphorylated, suggesting that multimerization is important for this proposed activity of the protein. The interaction domain with NSP6 was found to be present in the 35 C-terminal aa of NSP5, overlapping the multimerization domain of the protein, and suggesting that NSP6 might have a regulatory role in the self-association of NSP5. NSP6 was also found to interact with wild-type NSP5, but not with its mutant ∆C10, in cells transiently transfected with plasmids encoding these proteins, confirming the relevance of the 10 C-terminal aa for the formation of the heterocomplex.

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The nucleotide sequence of 1.7 kbp cDNA, comprising the region nearest the 3' end of the genome of the porcine epidemic diarrhoea virus (PEDV), has been independently determined for two European isolates of PEDV. Almost identical results were obtained for the two isolates, which were derived from cases of PEDV infection in Belgium and Britain in 1977 and 1987, respectively. The sequences contained a 1323 nucleotide (nt) open reading frame (ORF), which showed moderate identity to the nucleocapsid (N) gene of other coronaviruses. The greatest similarity at both the nucleic acid and protein levels was to the human coronavirus 229E.The PEDV N gene was, however, notably larger than that of the human 229E and porcine transmissible gastroenteritis viruses. This reflects the presence of a putative insertion of approximately 135 nt located towards the middle of the N gene. A second 336 nt ORF, which might encode a leucine-rich protein similar to, but shorter than, the bovine coronavirus internal protein was found within the PEDV N gene. Several RNA motifs typical of coronaviruses were also observed. These results confirm the earlier provisional classification of PEDV as a coronavirus.

Escherichia coli LR05, in addition to producing MccB17, J25, and D93, secretes microcin L, a newly discovered microcin that exhibits strong antibacterial activity against related Enterobacteriaceae, including Salmonella enterica serovars Typhimurium and Enteritidis. Microcin L was purified using a two-step procedure including solid-phase extraction and reverse-phase C 18 high-performance liquid chromatography. A 4,901-bp region of the DNA plasmid of E. coli LR05 was sequenced revealing that the microcin L cluster consists of four genes, mclC, mclI, mclA, and mclB. As bacterial resistance to currently used antibiotics is increasing, new pathogenic agents are discovered, and traditional bacterial diseases reappear, increased efforts to search for new antibiotics are needed. Over the past 40 years, research has been restricted largely to improving those well-known compound classes that are active against a standard set of drug targets. As no new classes of antibiotic have been discovered, such insufficient chemical variability exists that there is a potential for serious escalation in clinical microbe resistance. Numerous living organisms are able to produce a variety of ribosomally synthesized antibacterial peptides or proteins involved in their innate defense against microorganisms. During the past 15 years, these compounds have attracted considerable attention, offering many exciting possibilities for the future of antibiotics, in the face of current declining efficacy of conventional treatment (20,22). Of the bacteriocins produced by bacteria, many direct activity against pathogens and, in particular, food-borne microorganisms, such as the grampositive bacterium Listeria monocytogenes (7, 10) and gramnegative bacteria Salmonella enterica and Escherichia coli (34,40).Microcins are secreted by members of the Enterobacteriaceae family, in particular strains of E. coli. They constitute a class of low-molecular-mass peptides (Ͻ10 kDa) that exhibit a narrow antimicrobial spectrum of activity directed against bacterial species phylogenetically related to the producing strains (33). To protect itself, the microcin-producing bacterium exhibits immunity to the action of its own microcin. Recent developments in the biochemical characterization and mode of action allowed us to propose a classification of these peptides into two classes (17, 36). Class I, which includes to date microcins B17, C7, D93, and J25, encompasses peptides with molecular mass below 5 kDa that are highly posttranslationally modified. These microcins display a range of unrelated chemical structures, which in turn results in a variety of action mechanisms (9). Class II includes microcins E492, H47, V, most likely microcin 24, and now microcin L. This second group is more homogeneous and shares several common structural properties with class IIa gram-positive bacteriocins: size ranging from 7 to 10 kDa, absence of modified amino acids, and presence of a consensus motif. Additionally, they are synthesized as precursor peptides with a double-glycine type ...

Double-stranded RNA-binding proteins constitute a large family with conserved domains called dsRBDs. One of these, TRBP, a protein that binds HIV-1 TAR RNA, has two dsRBDs (dsRBD1 and dsRBD2), as indicated by computer sequence homology. However, a 24-amino-acid deletion in dsRBD2 completely abolishes RNA binding, suggesting that only one domain is functional. To analyse further the similarities and differences between these domains, we expressed them independently and measured their RNA-binding affinities. We found that dsRBD2 has a dissociation constant of 5.9 Â 10 28 m, whereas dsRBD1 binds RNA minimally. Binding analysis of 25-amino-acid peptides in TRBP and other related proteins showed that only one peptide in TRBP and one in Drosophila Staufen bind TAR and a GC-rich TAR-mimic RNA. Whereas a 25-mer peptide derived from dsRBD2 (TR5) bound TAR RNA, the equivalent peptide in dsRBD1 (TR6) did not. Molecular modelling indicates that this difference can mainly be ascribed to the replacement of Arg by His residues. Mutational analyses in homologous peptides also show the importance of residues K2 and L3. Analysis of 15-amino-acid peptides revealed that, in addition to TR13 (from TRBP dsRBD2), one peptide in S6 kinase has RNA-binding properties. On the basis of previous and the present results, we can define, in a broader context than that of TRBP, the main outlines of a modular KR-helix motif required for binding TAR. This structural motif exists independently from the dsRBD context and therefore has a modular function.Keywords: dsRNA-binding domain (dsRBD); peptide motif; RNA±protein interaction; TAR; TAR RNA-binding protein (TRBP).RNA-binding proteins are found in a wide spectrum of organisms from virus to mammalian cells. They play key roles in gene expression and regulation. Families of proteins are defined by either large domains or smaller motifs that mediate RNA binding [1]. Among the large domains, the RNA recognition motif is composed of 90±100 amino acids [2,3], the KH domain (based on hnRNP K homology) consists of 70±100 hydrophobic-rich amino acids [4], and the cold shock domain, 65±70 amino-acid residues long, binds to RNA and ssDNA [5]. The dsRNA-binding domains (dsRBDs) consist of 65±70 amino acids [6±8], are found in a large variety of RNA-binding proteins and mediate dsRNA interactions. The structures of four dsRBDs have been determined by NMR or crystallography and have an a-b-b-b-a topology [8±11]. Whereas some of these proteins appear to bind RNA in a sequence-independent manner [10], most functions seem to be related to binding specificity determined by motifs adjacent to the dsRBDs or by particular sequence features within the domain [12,13].Small motifs can be responsible, in part, for specificity. Zinc fingers are 30-amino-acid motifs described in many DNA-binding proteins but are also present in RNA-binding proteins, including TFIIIA, retroviral nucleocapsids and large subunits of RNA polymerases [14,15]. Arginine-rich motifs found in retroviral Rev, Rex and Tat, bacteriophage N and riboso...