Serratia nevei 9rpt1, a Potential Microorganism for Phosphorus Recovery

Aims: Phosphorus (P) is an essential element for life, finite and irreplaceable. Its constant exploration on a global scale has motivated frequent alerts regarding an eventual crisis due to the shortage of this nutrient. However, it is possible to recycle it and reintroduce it into the ecological cycle. One viable alternative is the microbial recovery of phosphate. Study design: This study is based on systematic bioprospection of bacteria in phosphate-deficient Amazon regions. Place and Duration of Study: Bacteria were isolated from black water samples, collected in the Rio Pretinho, located at Serra do Aracá, Barcelos, Amazonas, Brazil, from January to July 2019. Methodology: Microbial isolation was performed in Luria Bertani agar medium. For the genomic study, the isolate with the best performance in the phosphate uptake test was chosen. The WGS was carried out in a Illumina HiSeq 2500 System. The assembly of the draft genome was carried out with the SPAdes and the annotation by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Results: Serratia nevei 9rpt1 recovers 90% of the phosphate available in the culture medium. Its draft genome comprises 5.4 MB, the GC content is 59.52% and 4,922 coding sequences were identified, among these, two pst operons: one complete, containing the five pst genes and one missing pstS, pstC and phoU genes. Conclusion: Serratia nevei 9rpt1, isolated from an Amazonian environment poor in phosphate, is very efficient to uptake this nutrient in a Pi starvation condition. The genomic findings revealed this strain has an additional high affinity Pi uptake pst system containing the ATP-binding protein PstB, the canonical permease PstA, a putative permease other than PstC, upstream of the PstA and two essential enzymes in the polyphosphate metabolism: polyphosphate kinase 1 and exopolyphosphatase.

Large cryptic internal sequence repeats in protein structures from Homo sapiens.

Amino acid sequences are known to constantly mutate and diverge unless there is a limiting condition that makes such a change deleterious. However, closer examination of the sequence and structure reveals that a few large, cryptic repeats are nevertheless sequentially conserved. This leads to the question of why only certain repeats are conserved at the sequence level. It would be interesting to fi nd out if these sequences maintain their conservation at the three-dimensional structure level. They can play an active role in protein and nucleotide stability, thus not only ensuring proper functioning but also potentiating malfunction and disease. Therefore, insights into any aspect of the repeats – be it structure, function or evolution – would prove to be of some importance. This study aims to address the relationship between protein sequence and its three-dimensional structure, by examining if large cryptic sequence repeats have the same structure.

Iterative ACORN as a high throughput tool in structural genomics.

High throughput macromolecular structure determination is very essential in structural genomics as the available number of sequence information far exceeds the number of available 3D structures. ACORN, a freely available resource in the CCP4 suite of programs is a comprehensive and efficient program for phasing in the determination of protein structures, when atomic resolution data are available. ACORN with the automatic model-building program ARP/wARP and refinement program REFMAC is a suitable combination for the high throughput structural genomics. ACORN can also be run with secondary structural elements like helices and sheets as inputs with high resolution data. In situations, where ACORN phasing is not sufficient for building the protein model, the fragments (incomplete model/dummy atoms) can again be used as a starting input. Iterative ACORN is proved to work efficiently in the subsequent model building stages in congerin (PDB-ID: lis3) and catalase (PDB-ID: 1gwe) for which models are available.

Crotacetin, a novel snake venom C-type lectin, is homolog of convulxin

Snake venom (sv) C-type lectins encompass a group of hemorrhagic toxins, which are able to interfere with hemostasis. They share significant similarity in their primary structures with C-type lectins of other animals, and also present a conserved carbohydrate recognition domain (CRD). A very well studied sv C-type lectin is the heterodimeric toxin, convulxin (CVX), from the venoms of South American rattlesnakes, Crotalus durissus terrificus and C. d. cascavella. It consists of two subunits, alfa (CVXa, 13.9 kDa) and beta (CVXb, 12.6 kDa), joined by inter and intra-chain disulfide bounds, and is arranged in a tetrameric a4b4 conformation. Convulxin is able to activate platelet and induce their aggregation by acting via p62/GPVI collagen receptor. Several cDNA precursors, homolog of CVX subunits, were cloned by PCR homology screening. As determined by computational analysis, one of them, named crotacetin b subunit, was predicted as a polypeptide with a tridimensional conformation very similar to other subunits of convulxin-like snake toxins. Crotacetin was purified from C. durissus venoms by gel permeation and reverse phase high performance liquid chromatography. The heterodimeric crotacetin is expressed in the venoms of several C. durissus subspecies, but it is prevalent in the venom of C. durissus cascavella. As inferred from homology modeling, crotacetin induces platelet aggregation but noticeably exhibits antimicrobial activity against Gram-positive and Gram-negative bacteria

HLA class II alleles in Japanese patients with non-Hodgkin's lymphoma.

The distribution of HLA-DRB1 alleles and DQB1 alleles in 30 Japanese patients with non-Hodgkin's lymphoma (NHL) was analyzed using polymerase chain reaction with the sequence-specific primer (PCR-SSP) method, and the association between the disease and the presence of certain HLA class II alleles was investigated. The frequencies of HLA-DRB1*0803, DRB1*0802 and DRB1*1502 were increased while those of DRB1*1501 and DRB1*0405 were decreased. On the other hand, the incidence of HLA-DQB1 alleles was similar to that in the normal population. However, none of these HLA class II alleles showed significant positive or negative associations with NHL. In addition, when allele frequencies of NHL Japanese patients were compared to Thai patients, only DRB1*0803 was significantly increased in Japanese patients. These results indicate that DRB1*0803 may not contribute to NHL susceptibility in the Japanese population. However, further studies with larger numbers of NHL Japanese patients are needed to confirm our preliminary findings.

Incidence of abnormalities in laboratory tests found in surveillance of adults over 40 years of age.

National health check-up systems have been used for 5 years in Japan for adults who are over 40 years of age. As part of a national project, Osaka prefecture is also conducting a program for health check-up testing and cancer screening for this age group. This surveillance revealed that incidence of obesity, hypertension, cholesterolemia, albuminuria, or abnormal ECG was high. Analysis of surveillance results should contribute to understanding the present status and recent trends in diseases in the aged. With continuation of this surveillance for a number of years, trends in life-style related diseases in Japan should be detectable.