I spent days scouring the php openssl documentation trying to figure out how to do what sounds like a simple task - given two PEM encoded certificates, is one the signer of the other? Nowhere in the openssl_verify() documentation or comments is it explained where to obtain the signature of an existing certificate. The openssl_x509_parse() function looked promising, but it is an unstable API that may change.
I had to write my own code to determine if one cert signed another, it is located here: http://badpenguins.com/source/misc/isCertSigner.php?viewSource
In a nutshell here is what I learned...
The signature data in a signed X.509 certificate contains DER formatted data about the signature that is encrypted with the signers public key. The data contains a hash of the original subject certificate and information about what encryption algorithm was used to create the signature.
So you need to get this signature data and a copy of the original certificate with the issuer and signature sequences removed. Hash a copy of the original certificate (sans issuer/signature sequences) with the same algorithm the issuer used and if the hashes match, you have the issuer cert that signed the certificate.