Biology subjects

Alsaleh, A.

Publications and source records attributed to Alsaleh, A..

3 recordsLinked to original sources

bioRxiv2024

Large serine integrases utilise scavenged phage proteins as directionality cofactors

Recombination directionality factors (RDFs) for large serine integrases (LSIs) are cofactor proteins that control the directionality of recombination to favor excision over insertion. Although RDFs are predicted to bind their cognate LSIs in similar ways, there is no overall common structural theme across LSI RDFs, leading to the suggestion that some of them may be moonlighting proteins with other primary functions. To test this hypothesis, we searched for characterized proteins with structures similar to the predicted structures of known RDFs. Our search shows that the RDFs for two LSIs, TG1 integrase and Bxb1 integrase, show high similarities to a single stranded DNA binding (SSB) protein and an editing exonuclease, respectively. We present experimental data to show that TG1 RDF is a functional SSB protein. We used mutational analysis to validate the integrase-RDF interface predicted by AlphaFold2 multimer for TG1 integrase and its RDF, and establish that control of recombination directionality is mediated via protein-protein interaction at the junction of recombinases second DNA binding domain and the base of the coiled coil domain.

molecular biology↗

bioRxiv2024

Identification of cognate recombination directionality factors for large serine recombinases by virtual pulldown

Integrases from the "large serine" family are simple, highly directional site-specific DNA recombinases that have great promise as synthetic biology and genome editing tools. Integrative recombination (mimicking phage or mobile element insertion) requires only integrase and two short ([~]40 - 50) DNA sites. The reverse reaction, excisive recombination, does not occur until it is triggered by the presence of a second protein termed a Recombination Directionality Factor (RDF), which binds specifically to its cognate integrase. Identification of RDFs has been hampered due to their lack of sequence conservation and lack of synteny with the phage integrase gene. Here we use Alphafold2-multimer to identify putative RDFs for more than half of a test set of 98 large serine recombinases, and experimental methods to verify predicted RDFs for 4 of 5 integrases chosen as test cases. We find no universally conserved structural motifs among known and predicted RDFs, yet they are all predicted to bind a similar location on their cognate integrase, suggesting convergent evolution of function. Our methodology greatly expands the available genetic toolkit of cognate integrase - RDF pairs.

synthetic biology↗

bioRxiv2019

Genetic diversity and haplotypic structure of a Saudi population sample using Investigator Argus X-12 amplification kit

X-chromosome short tandem repeat (X-STR) markers have shown a great capability in forensic identity investigations and paternity testing involving kinship analysis.\n\nIn the current study, the distribution of 12 X-STR loci located in four linkage groups was evaluated using Investigator(R) Argus X-12 Amplification Kit in 200 unrelated healthy individuals (105 males and 95 females) from the central region of the Saudi Arabia in order to create a DNA database.\n\nOur results indicated that DXS10146 locus was the most informative with 21 alleles while DXS8378 locus was the least with five alleles. Forensic parameters showed that all X-STRs loci either as individual markers or as linkage groups provide genetic information with high discrimination that is appropriate for forensic purposes with Paternity Informed Consent (PIC), Power of exclusion (PE), and Paternity index (PI) varied from 0.61211 to 0.917979, 0.38722 to 0.842949, and 0.038416 to 0.16367, respectively. A significant Linkage disequilibrium (LD) with p-value after Bonferroni correction p [≤] 0.05/66= 0.0008 was observed for 17 pairs of loci in male samples and 4 pairs of loci in female. In the male group, LG3 showed relatively high values of Haplotype diversity. The pairwise genetic distance fixation index (Fst) results showed that the Saudi population is genetically close to the Egyptian and Emirati populations and distant to the Turkish population.\n\nThe current study revealed that Investigator(R) Argus 12 X-STR kit would support forensic application, kinship testing involving female offspring, and human identification in Saudi populations.

genetics↗